Starting phenix.real_space_refine on Sun Mar 17 15:08:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5it9_8124/03_2024/5it9_8124.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5it9_8124/03_2024/5it9_8124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5it9_8124/03_2024/5it9_8124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5it9_8124/03_2024/5it9_8124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5it9_8124/03_2024/5it9_8124.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5it9_8124/03_2024/5it9_8124.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1972 5.49 5 Mg 80 5.21 5 S 80 5.16 5 C 42857 2.51 5 N 14479 2.21 5 O 20673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 34": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "G PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H GLU 184": "OE1" <-> "OE2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K GLU 33": "OE1" <-> "OE2" Residue "K GLU 84": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "N GLU 119": "OE1" <-> "OE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P GLU 69": "OE1" <-> "OE2" Residue "P GLU 110": "OE1" <-> "OE2" Residue "P GLU 118": "OE1" <-> "OE2" Residue "Q GLU 99": "OE1" <-> "OE2" Residue "Q GLU 104": "OE1" <-> "OE2" Residue "S GLU 60": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S GLU 106": "OE1" <-> "OE2" Residue "S GLU 114": "OE1" <-> "OE2" Residue "T PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 109": "OE1" <-> "OE2" Residue "T GLU 115": "OE1" <-> "OE2" Residue "U GLU 35": "OE1" <-> "OE2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "V GLU 49": "OE1" <-> "OE2" Residue "V GLU 64": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W GLU 49": "OE1" <-> "OE2" Residue "W GLU 115": "OE1" <-> "OE2" Residue "X GLU 55": "OE1" <-> "OE2" Residue "X GLU 98": "OE1" <-> "OE2" Residue "X GLU 101": "OE1" <-> "OE2" Residue "Y GLU 98": "OE1" <-> "OE2" Residue "Z ARG 68": "NH1" <-> "NH2" Residue "Z GLU 84": "OE1" <-> "OE2" Residue "c GLU 58": "OE1" <-> "OE2" Residue "c GLU 62": "OE1" <-> "OE2" Residue "d GLU 4": "OE1" <-> "OE2" Residue "f GLU 111": "OE1" <-> "OE2" Residue "g GLU 15": "OE1" <-> "OE2" Residue "g GLU 50": "OE1" <-> "OE2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g GLU 246": "OE1" <-> "OE2" Residue "g GLU 275": "OE1" <-> "OE2" Residue "g GLU 280": "OE1" <-> "OE2" Residue "g GLU 284": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 80144 Number of models: 1 Model: "" Number of chains: 43 Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1616 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 16, 'TRANS': 189} Chain: "B" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1722 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "C" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1629 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "D" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1744 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain: "E" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2078 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 13, 'TRANS': 246} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1609 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "G" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1812 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "H" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1483 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain: "I" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1493 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "J" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1471 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "K" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 809 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "L" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "M" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 922 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "N" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1187 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "O" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 942 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "P" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 114} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1105 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "R" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1031 Classifications: {'peptide': 129} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 122} Chain: "S" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1193 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "T" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1110 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "U" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 845 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "V" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 687 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "W" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "X" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1127 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "Y" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1061 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Z" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 558 Classifications: {'peptide': 70} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 64} Chain: "a" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 798 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "b" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 617 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "c" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 494 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "d" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "e" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 443 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 5, 'TRANS': 49} Chain: "f" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 65} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2466 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain breaks: 2 Chain: "2" Number of atoms: 37797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1780, 37797 Classifications: {'RNA': 1780} Modifications used: {'rna2p_pur': 151, 'rna2p_pyr': 154, 'rna3p_pur': 786, 'rna3p_pyr': 689} Link IDs: {'rna2p': 305, 'rna3p': 1474} Chain breaks: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {' G%rna3p_pur:plan2': 5, ' C%rna3p_pyr:plan': 4, ' A%rna3p_pur:plan2': 4, ' U%rna3p_pyr:plan': 1, ' C%rna3p_pyr:plan2': 4, ' G%rna3p_pur:plan': 5, ' A%rna3p_pur:plan': 4} Unresolved non-hydrogen planarities: 161 Chain: "i" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3968 Classifications: {'DNA': 6, 'RNA': 186} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 16, 'rna3p_pur': 76, 'rna3p_pyr': 81} Link IDs: {'rna2p': 27, 'rna3p': 164} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {' U:plan': 1, ' G:plan2': 1, ' A:plan': 5, ' G:plan': 1, ' A:plan2': 5} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Unusual residues: {' MG': 76} Classifications: {'undetermined': 76} Link IDs: {None: 75} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 32663 SG CYS a 23 118.401 113.897 142.954 1.00 10.83 S ATOM 32684 SG CYS a 26 118.384 112.602 138.647 1.00 9.64 S ATOM 33066 SG CYS a 74 118.800 116.136 139.191 1.00 13.53 S ATOM 33730 SG CYS b 59 138.810 156.630 198.389 1.00158.49 S Time building chain proxies: 33.23, per 1000 atoms: 0.41 Number of scatterers: 80144 At special positions: 0 Unit cell: (246.56, 258.62, 210.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 80 16.00 P 1972 15.00 Mg 80 11.99 O 20673 8.00 N 14479 7.00 C 42857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 39926 O5' A 2 78 .*. O " rejected from bonding due to valence issues. Atom "ATOM 39926 O5' A 2 78 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.15 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 201 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 23 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 74 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 26 " pdb=" ZN b 101 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 59 " 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9018 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 58 sheets defined 34.5% alpha, 16.1% beta 518 base pairs and 905 stacking pairs defined. Time for finding SS restraints: 24.74 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 49 through 67 removed outlier: 3.617A pdb=" N THR A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 removed outlier: 3.824A pdb=" N GLN A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ALA A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.703A pdb=" N SER B 60 " --> pdb=" O ASN B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.714A pdb=" N HIS B 79 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.908A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 181 through 189 Processing helix chain 'B' and resid 191 through 202 Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.760A pdb=" N HIS B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 53 Processing helix chain 'C' and resid 57 through 64 removed outlier: 4.180A pdb=" N ILE C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 removed outlier: 3.744A pdb=" N ASP C 75 " --> pdb=" O PHE C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 141 Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 211 through 227 removed outlier: 4.157A pdb=" N TYR C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.618A pdb=" N TRP C 235 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'D' and resid 6 through 29 Processing helix chain 'D' and resid 54 through 60 Processing helix chain 'D' and resid 64 through 78 Processing helix chain 'D' and resid 98 through 112 Processing helix chain 'D' and resid 114 through 130 Processing helix chain 'D' and resid 192 through 195 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.519A pdb=" N SER E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 50 Processing helix chain 'E' and resid 57 through 68 Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.979A pdb=" N ASN E 188 " --> pdb=" O GLY E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 258 Processing helix chain 'F' and resid 32 through 38 Processing helix chain 'F' and resid 84 through 89 removed outlier: 4.047A pdb=" N GLN F 88 " --> pdb=" O PHE F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 100 Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 108 through 126 Processing helix chain 'F' and resid 130 through 143 Processing helix chain 'F' and resid 165 through 186 Processing helix chain 'F' and resid 191 through 205 Processing helix chain 'F' and resid 210 through 226 Processing helix chain 'G' and resid 20 through 25 removed outlier: 3.739A pdb=" N VAL G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 148 through 152 removed outlier: 3.567A pdb=" N ASP G 151 " --> pdb=" O THR G 148 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP G 152 " --> pdb=" O LYS G 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 148 through 152' Processing helix chain 'G' and resid 180 through 224 Processing helix chain 'H' and resid 14 through 29 Processing helix chain 'H' and resid 33 through 40 Processing helix chain 'H' and resid 66 through 74 Processing helix chain 'H' and resid 74 through 85 Processing helix chain 'H' and resid 117 through 130 Processing helix chain 'H' and resid 161 through 177 removed outlier: 4.392A pdb=" N LYS H 165 " --> pdb=" O HIS H 161 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU H 167 " --> pdb=" O ASP H 163 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER H 168 " --> pdb=" O ASN H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 93 Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 137 through 147 removed outlier: 4.084A pdb=" N ARG I 142 " --> pdb=" O LYS I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 164 Processing helix chain 'I' and resid 173 through 178 Processing helix chain 'I' and resid 186 through 201 removed outlier: 3.776A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 34 Processing helix chain 'J' and resid 38 through 62 removed outlier: 4.125A pdb=" N ILE J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 84 Processing helix chain 'J' and resid 100 through 107 removed outlier: 3.658A pdb=" N PHE J 104 " --> pdb=" O LYS J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 115 removed outlier: 3.879A pdb=" N TYR J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 131 Processing helix chain 'J' and resid 171 through 183 Processing helix chain 'K' and resid 4 through 19 removed outlier: 3.614A pdb=" N ARG K 8 " --> pdb=" O PRO K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 52 Processing helix chain 'K' and resid 59 through 61 No H-bonds generated for 'chain 'K' and resid 59 through 61' Processing helix chain 'K' and resid 69 through 81 Processing helix chain 'L' and resid 45 through 51 removed outlier: 3.571A pdb=" N ILE L 49 " --> pdb=" O PRO L 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 32 Processing helix chain 'M' and resid 37 through 47 Processing helix chain 'M' and resid 59 through 61 No H-bonds generated for 'chain 'M' and resid 59 through 61' Processing helix chain 'M' and resid 62 through 75 removed outlier: 4.356A pdb=" N ASN M 75 " --> pdb=" O LEU M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 121 through 133 removed outlier: 4.252A pdb=" N GLU M 125 " --> pdb=" O THR M 121 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE M 126 " --> pdb=" O GLN M 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 Processing helix chain 'N' and resid 46 through 58 removed outlier: 3.527A pdb=" N ALA N 57 " --> pdb=" O LEU N 53 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 71 through 79 Processing helix chain 'N' and resid 85 through 105 Processing helix chain 'N' and resid 108 through 133 Processing helix chain 'N' and resid 143 through 151 removed outlier: 3.839A pdb=" N SER N 147 " --> pdb=" O SER N 143 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA N 148 " --> pdb=" O ALA N 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 48 removed outlier: 3.746A pdb=" N LYS O 47 " --> pdb=" O THR O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 75 Processing helix chain 'O' and resid 96 through 109 removed outlier: 4.508A pdb=" N ALA O 100 " --> pdb=" O PRO O 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 26 removed outlier: 4.116A pdb=" N LEU P 25 " --> pdb=" O ASP P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 36 removed outlier: 4.114A pdb=" N ASP P 32 " --> pdb=" O MET P 28 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE P 33 " --> pdb=" O PRO P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 47 Processing helix chain 'P' and resid 54 through 66 removed outlier: 3.737A pdb=" N LYS P 58 " --> pdb=" O ALA P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.751A pdb=" N MET P 89 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 86 through 90' Processing helix chain 'P' and resid 116 through 120 removed outlier: 3.724A pdb=" N SER P 120 " --> pdb=" O GLY P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 56 Proline residue: Q 51 - end of helix Processing helix chain 'Q' and resid 57 through 61 Processing helix chain 'Q' and resid 74 through 97 removed outlier: 3.545A pdb=" N LEU Q 89 " --> pdb=" O ILE Q 85 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL Q 90 " --> pdb=" O ALA Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 112 removed outlier: 3.768A pdb=" N LYS Q 102 " --> pdb=" O ASP Q 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 27 through 39 removed outlier: 3.625A pdb=" N ASN R 31 " --> pdb=" O ASP R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 63 Processing helix chain 'R' and resid 72 through 84 removed outlier: 3.551A pdb=" N LYS R 81 " --> pdb=" O GLU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 114 Processing helix chain 'S' and resid 27 through 35 Processing helix chain 'S' and resid 39 through 51 Processing helix chain 'S' and resid 62 through 75 Processing helix chain 'S' and resid 102 through 120 Processing helix chain 'S' and resid 121 through 130 Processing helix chain 'T' and resid 11 through 26 Processing helix chain 'T' and resid 53 through 68 Processing helix chain 'T' and resid 72 through 81 Processing helix chain 'T' and resid 97 through 112 Processing helix chain 'T' and resid 125 through 144 Processing helix chain 'U' and resid 30 through 49 removed outlier: 3.600A pdb=" N LEU U 34 " --> pdb=" O LYS U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 106 removed outlier: 3.560A pdb=" N VAL U 100 " --> pdb=" O PRO U 96 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 63 removed outlier: 3.711A pdb=" N ARG V 60 " --> pdb=" O SER V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 77 Processing helix chain 'W' and resid 5 through 21 Processing helix chain 'W' and resid 31 through 45 Processing helix chain 'W' and resid 84 through 94 removed outlier: 4.016A pdb=" N LYS W 88 " --> pdb=" O ALA W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 120 Processing helix chain 'X' and resid 11 through 24 removed outlier: 3.653A pdb=" N TRP X 24 " --> pdb=" O ARG X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 35 Processing helix chain 'X' and resid 35 through 40 Processing helix chain 'X' and resid 92 through 97 Processing helix chain 'X' and resid 131 through 138 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 95 Processing helix chain 'Y' and resid 104 through 118 Processing helix chain 'Y' and resid 121 through 135 removed outlier: 4.186A pdb=" N ILE Y 125 " --> pdb=" O THR Y 121 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA Y 134 " --> pdb=" O ALA Y 130 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP Y 135 " --> pdb=" O ARG Y 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 52 Processing helix chain 'Z' and resid 61 through 66 Processing helix chain 'Z' and resid 72 through 84 removed outlier: 3.566A pdb=" N ALA Z 76 " --> pdb=" O GLY Z 72 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 57 removed outlier: 4.078A pdb=" N ASP a 52 " --> pdb=" O ALA a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 80 Processing helix chain 'a' and resid 89 through 94 removed outlier: 3.774A pdb=" N ARG a 93 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 18 removed outlier: 3.658A pdb=" N GLU b 15 " --> pdb=" O THR b 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 32 through 36 removed outlier: 3.682A pdb=" N GLY d 35 " --> pdb=" O ARG d 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 47 Processing helix chain 'e' and resid 12 through 18 removed outlier: 3.903A pdb=" N SER e 16 " --> pdb=" O GLY e 12 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR e 18 " --> pdb=" O VAL e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 44 removed outlier: 3.827A pdb=" N LYS e 36 " --> pdb=" O GLY e 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.532A pdb=" N VAL A 74 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 121 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL A 143 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ALA A 159 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA A 145 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.886A pdb=" N LEU B 96 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B 91 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR B 98 " --> pdb=" O ASP B 89 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASP B 89 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE B 100 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 120 through 121 removed outlier: 6.801A pdb=" N PHE B 142 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASN B 209 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 128 Processing sheet with id=AA5, first strand: chain 'C' and resid 82 through 94 removed outlier: 6.844A pdb=" N VAL C 106 " --> pdb=" O MET C 86 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE C 88 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LYS C 104 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG C 102 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN C 92 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ARG C 100 " --> pdb=" O GLN C 92 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 123 " --> pdb=" O PHE C 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 147 removed outlier: 3.541A pdb=" N SER C 158 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 163 through 164 Processing sheet with id=AA8, first strand: chain 'C' and resid 170 through 171 Processing sheet with id=AA9, first strand: chain 'D' and resid 34 through 41 Processing sheet with id=AB1, first strand: chain 'D' and resid 148 through 155 Processing sheet with id=AB2, first strand: chain 'D' and resid 223 through 224 removed outlier: 5.418A pdb=" N ILE g 195 " --> pdb=" O SER g 187 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER g 187 " --> pdb=" O ILE g 195 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA g 197 " --> pdb=" O SER g 185 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL g 183 " --> pdb=" O PHE g 199 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE g 174 " --> pdb=" O TRP g 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR g 173 " --> pdb=" O ALA g 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 9 through 10 removed outlier: 4.221A pdb=" N LEU E 9 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 70 through 72 removed outlier: 3.539A pdb=" N LEU E 92 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN E 98 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N HIS E 112 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.596A pdb=" N ASP E 171 " --> pdb=" O LYS E 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 128 through 131 removed outlier: 3.599A pdb=" N LYS E 128 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 192 through 193 Processing sheet with id=AB8, first strand: chain 'E' and resid 207 through 211 Processing sheet with id=AB9, first strand: chain 'E' and resid 229 through 230 Processing sheet with id=AC1, first strand: chain 'F' and resid 146 through 150 removed outlier: 3.541A pdb=" N GLN F 160 " --> pdb=" O THR F 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 12 through 17 removed outlier: 3.692A pdb=" N THR G 12 " --> pdb=" O TYR G 7 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE G 5 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU G 106 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP G 57 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL G 108 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLY G 55 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA G 110 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL G 49 " --> pdb=" O THR G 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AC4, first strand: chain 'G' and resid 160 through 163 Processing sheet with id=AC5, first strand: chain 'H' and resid 45 through 50 removed outlier: 3.573A pdb=" N SER H 45 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS H 56 " --> pdb=" O HIS H 89 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE H 91 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU H 58 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU H 93 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL H 60 " --> pdb=" O LEU H 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 180 through 184 removed outlier: 4.218A pdb=" N GLN H 180 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU W 49 " --> pdb=" O GLN W 64 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 42 through 44 Processing sheet with id=AC8, first strand: chain 'I' and resid 47 through 48 Processing sheet with id=AC9, first strand: chain 'I' and resid 78 through 83 removed outlier: 6.666A pdb=" N VAL I 81 " --> pdb=" O GLN I 103 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN I 103 " --> pdb=" O VAL I 81 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 21 through 24 Processing sheet with id=AD2, first strand: chain 'L' and resid 70 through 77 removed outlier: 3.899A pdb=" N THR L 74 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL L 85 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N PHE L 137 " --> pdb=" O ASN L 106 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL L 139 " --> pdb=" O PRO L 108 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N HIS L 110 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N LYS L 141 " --> pdb=" O HIS L 110 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL L 139 " --> pdb=" O GLY L 126 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLY L 126 " --> pdb=" O VAL L 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 90 through 94 removed outlier: 3.533A pdb=" N VAL L 94 " --> pdb=" O ARG L 99 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG L 99 " --> pdb=" O VAL L 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 34 through 36 removed outlier: 3.675A pdb=" N LEU M 52 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 25 through 26 removed outlier: 3.763A pdb=" N ASP O 25 " --> pdb=" O SER O 22 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 30 through 31 removed outlier: 6.677A pdb=" N VAL O 30 " --> pdb=" O ILE O 39 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 78 through 79 Processing sheet with id=AD8, first strand: chain 'P' and resid 76 through 78 Processing sheet with id=AD9, first strand: chain 'Q' and resid 7 through 13 Processing sheet with id=AE1, first strand: chain 'S' and resid 15 through 17 Processing sheet with id=AE2, first strand: chain 'T' and resid 114 through 116 Processing sheet with id=AE3, first strand: chain 'U' and resid 51 through 68 removed outlier: 7.793A pdb=" N LYS U 53 " --> pdb=" O GLU U 94 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLU U 94 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASP U 92 " --> pdb=" O PRO U 55 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ARG U 57 " --> pdb=" O TYR U 90 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR U 90 " --> pdb=" O ARG U 57 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LYS U 88 " --> pdb=" O PRO U 59 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 51 through 68 removed outlier: 7.793A pdb=" N LYS U 53 " --> pdb=" O GLU U 94 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLU U 94 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASP U 92 " --> pdb=" O PRO U 55 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ARG U 57 " --> pdb=" O TYR U 90 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR U 90 " --> pdb=" O ARG U 57 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LYS U 88 " --> pdb=" O PRO U 59 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 32 through 37 Processing sheet with id=AE6, first strand: chain 'W' and resid 109 through 111 Processing sheet with id=AE7, first strand: chain 'X' and resid 48 through 57 removed outlier: 5.684A pdb=" N VAL X 53 " --> pdb=" O GLN X 75 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN X 75 " --> pdb=" O VAL X 53 " (cutoff:3.500A) removed outlier: 10.491A pdb=" N PHE X 122 " --> pdb=" O LYS X 82 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR X 84 " --> pdb=" O PHE X 122 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL X 124 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE X 86 " --> pdb=" O VAL X 124 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N LYS X 126 " --> pdb=" O PHE X 86 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU X 103 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL X 127 " --> pdb=" O GLU X 101 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLU X 101 " --> pdb=" O VAL X 127 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 7 through 15 removed outlier: 5.471A pdb=" N ILE Y 7 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 7 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR Y 9 " --> pdb=" O ASP Y 26 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASP Y 26 " --> pdb=" O THR Y 9 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS Y 11 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL Y 24 " --> pdb=" O LYS Y 11 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 89 through 91 Processing sheet with id=AF1, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AF2, first strand: chain 'a' and resid 37 through 43 Processing sheet with id=AF3, first strand: chain 'b' and resid 43 through 47 removed outlier: 3.537A pdb=" N SER b 78 " --> pdb=" O LYS b 36 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'b' and resid 64 through 65 Processing sheet with id=AF5, first strand: chain 'c' and resid 39 through 44 removed outlier: 4.097A pdb=" N VAL c 25 " --> pdb=" O THR c 19 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY c 17 " --> pdb=" O GLN c 27 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG c 29 " --> pdb=" O VAL c 15 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL c 15 " --> pdb=" O ARG c 29 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLU c 31 " --> pdb=" O ILE c 13 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE c 13 " --> pdb=" O GLU c 31 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AF7, first strand: chain 'f' and resid 131 through 133 removed outlier: 3.716A pdb=" N TYR f 138 " --> pdb=" O ALA f 131 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG f 136 " --> pdb=" O HIS f 133 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 9 through 14 removed outlier: 5.476A pdb=" N LEU g 10 " --> pdb=" O GLN g 321 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN g 321 " --> pdb=" O LEU g 10 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 23 through 25 removed outlier: 6.446A pdb=" N ARG g 47 " --> pdb=" O PRO g 58 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 69 through 74 removed outlier: 3.603A pdb=" N ALA g 81 " --> pdb=" O TRP g 93 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU g 90 " --> pdb=" O PHE g 104 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASN g 94 " --> pdb=" O SER g 100 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N SER g 100 " --> pdb=" O ASN g 94 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 111 through 115 removed outlier: 3.883A pdb=" N TYR g 143 " --> pdb=" O VAL g 134 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'g' and resid 206 through 211 removed outlier: 4.776A pdb=" N GLY g 222 " --> pdb=" O GLN g 226 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLN g 226 " --> pdb=" O GLY g 222 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET g 239 " --> pdb=" O VAL g 229 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASN g 231 " --> pdb=" O ALA g 237 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ALA g 237 " --> pdb=" O ASN g 231 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'g' and resid 247 through 252 removed outlier: 6.745A pdb=" N ALA g 262 " --> pdb=" O PHE g 248 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU g 250 " --> pdb=" O THR g 260 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR g 260 " --> pdb=" O LEU g 250 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE g 252 " --> pdb=" O TRP g 258 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N TRP g 258 " --> pdb=" O PHE g 252 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ASP g 271 " --> pdb=" O LEU g 277 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU g 277 " --> pdb=" O ASP g 271 " (cutoff:3.500A) 1487 hydrogen bonds defined for protein. 4245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1267 hydrogen bonds 2128 hydrogen bond angles 0 basepair planarities 518 basepair parallelities 905 stacking parallelities Total time for adding SS restraints: 60.34 Time building geometry restraints manager: 34.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 8144 1.28 - 1.41: 26332 1.41 - 1.55: 46347 1.55 - 1.68: 4689 1.68 - 1.82: 128 Bond restraints: 85640 Sorted by residual: bond pdb=" CA ARG G 154 " pdb=" C ARG G 154 " ideal model delta sigma weight residual 1.523 1.712 -0.189 1.34e-02 5.57e+03 1.98e+02 bond pdb=" N ARG G 154 " pdb=" CA ARG G 154 " ideal model delta sigma weight residual 1.457 1.575 -0.118 1.29e-02 6.01e+03 8.34e+01 bond pdb=" O3' U 2 934 " pdb=" P G 2 935 " ideal model delta sigma weight residual 1.607 1.485 0.122 1.50e-02 4.44e+03 6.63e+01 bond pdb=" N ASN S 93 " pdb=" CA ASN S 93 " ideal model delta sigma weight residual 1.457 1.559 -0.102 1.29e-02 6.01e+03 6.22e+01 bond pdb=" O3' C i6109 " pdb=" P U i6110 " ideal model delta sigma weight residual 1.607 1.491 0.116 1.50e-02 4.44e+03 5.97e+01 ... (remaining 85635 not shown) Histogram of bond angle deviations from ideal: 88.93 - 98.84: 4 98.84 - 108.74: 23416 108.74 - 118.65: 56607 118.65 - 128.55: 42428 128.55 - 138.46: 2706 Bond angle restraints: 125161 Sorted by residual: angle pdb=" N ARG Z 68 " pdb=" CA ARG Z 68 " pdb=" C ARG Z 68 " ideal model delta sigma weight residual 112.92 88.93 23.99 1.23e+00 6.61e-01 3.80e+02 angle pdb=" O3' C 21074 " pdb=" C3' C 21074 " pdb=" C2' C 21074 " ideal model delta sigma weight residual 113.70 134.03 -20.33 1.50e+00 4.44e-01 1.84e+02 angle pdb=" C4' A 2 78 " pdb=" C3' A 2 78 " pdb=" O3' A 2 78 " ideal model delta sigma weight residual 113.00 128.88 -15.88 1.50e+00 4.44e-01 1.12e+02 angle pdb=" O3' G 21534 " pdb=" C3' G 21534 " pdb=" C2' G 21534 " ideal model delta sigma weight residual 109.50 123.36 -13.86 1.50e+00 4.44e-01 8.54e+01 angle pdb=" C4' A 21075 " pdb=" C3' A 21075 " pdb=" O3' A 21075 " ideal model delta sigma weight residual 109.40 122.70 -13.30 1.50e+00 4.44e-01 7.86e+01 ... (remaining 125156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 47438 35.97 - 71.94: 6096 71.94 - 107.91: 621 107.91 - 143.88: 35 143.88 - 179.85: 81 Dihedral angle restraints: 54271 sinusoidal: 40295 harmonic: 13976 Sorted by residual: dihedral pdb=" C5' G 21534 " pdb=" C4' G 21534 " pdb=" C3' G 21534 " pdb=" O3' G 21534 " ideal model delta sinusoidal sigma weight residual 147.00 67.47 79.53 1 8.00e+00 1.56e-02 1.23e+02 dihedral pdb=" C5' A 21243 " pdb=" C4' A 21243 " pdb=" C3' A 21243 " pdb=" O3' A 21243 " ideal model delta sinusoidal sigma weight residual 147.00 69.05 77.95 1 8.00e+00 1.56e-02 1.19e+02 dihedral pdb=" C5' A 21501 " pdb=" C4' A 21501 " pdb=" C3' A 21501 " pdb=" O3' A 21501 " ideal model delta sinusoidal sigma weight residual 147.00 71.48 75.52 1 8.00e+00 1.56e-02 1.12e+02 ... (remaining 54268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.284: 15557 0.284 - 0.567: 150 0.567 - 0.851: 8 0.851 - 1.135: 0 1.135 - 1.418: 1 Chirality restraints: 15716 Sorted by residual: chirality pdb=" C3' C 21074 " pdb=" C4' C 21074 " pdb=" O3' C 21074 " pdb=" C2' C 21074 " both_signs ideal model delta sigma weight residual False -2.48 -1.06 -1.42 2.00e-01 2.50e+01 5.03e+01 chirality pdb=" CA PHE G 145 " pdb=" N PHE G 145 " pdb=" C PHE G 145 " pdb=" CB PHE G 145 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" C3' C 2 269 " pdb=" C4' C 2 269 " pdb=" O3' C 2 269 " pdb=" C2' C 2 269 " both_signs ideal model delta sigma weight residual False -2.74 -2.02 -0.73 2.00e-01 2.50e+01 1.32e+01 ... (remaining 15713 not shown) Planarity restraints: 8655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 21073 " 0.057 2.00e-02 2.50e+03 1.26e-01 4.76e+02 pdb=" N9 G 21073 " 0.015 2.00e-02 2.50e+03 pdb=" C8 G 21073 " -0.010 2.00e-02 2.50e+03 pdb=" N7 G 21073 " -0.022 2.00e-02 2.50e+03 pdb=" C5 G 21073 " -0.034 2.00e-02 2.50e+03 pdb=" C6 G 21073 " -0.103 2.00e-02 2.50e+03 pdb=" O6 G 21073 " 0.229 2.00e-02 2.50e+03 pdb=" N1 G 21073 " -0.183 2.00e-02 2.50e+03 pdb=" C2 G 21073 " -0.204 2.00e-02 2.50e+03 pdb=" N2 G 21073 " 0.215 2.00e-02 2.50e+03 pdb=" N3 G 21073 " 0.021 2.00e-02 2.50e+03 pdb=" C4 G 21073 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21074 " 0.198 2.00e-02 2.50e+03 1.21e-01 3.30e+02 pdb=" N1 C 21074 " -0.074 2.00e-02 2.50e+03 pdb=" C2 C 21074 " -0.044 2.00e-02 2.50e+03 pdb=" O2 C 21074 " 0.022 2.00e-02 2.50e+03 pdb=" N3 C 21074 " -0.162 2.00e-02 2.50e+03 pdb=" C4 C 21074 " -0.037 2.00e-02 2.50e+03 pdb=" N4 C 21074 " 0.222 2.00e-02 2.50e+03 pdb=" C5 C 21074 " -0.065 2.00e-02 2.50e+03 pdb=" C6 C 21074 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Z 68 " 1.042 9.50e-02 1.11e+02 4.67e-01 1.32e+02 pdb=" NE ARG Z 68 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG Z 68 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG Z 68 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG Z 68 " 0.023 2.00e-02 2.50e+03 ... (remaining 8652 not shown) Histogram of nonbonded interaction distances: 0.71 - 1.55: 9 1.55 - 2.39: 282 2.39 - 3.23: 74881 3.23 - 4.06: 245667 4.06 - 4.90: 381064 Warning: very small nonbonded interaction distances. Nonbonded interactions: 701903 Sorted by model distance: nonbonded pdb=" NZ LYS e 53 " pdb=" N4 C i6221 " model vdw 0.713 3.200 nonbonded pdb=" C2 C 21044 " pdb=" O6 G 21073 " model vdw 0.957 3.260 nonbonded pdb=" N3 C 21044 " pdb=" O6 G 21073 " model vdw 0.959 2.496 nonbonded pdb=" N2 G 21073 " pdb=" N3 C 21074 " model vdw 1.066 2.600 nonbonded pdb=" N2 G 21073 " pdb=" C4 C 21074 " model vdw 1.256 3.340 ... (remaining 701898 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 8.300 Check model and map are aligned: 0.900 Set scattering table: 0.570 Process input model: 222.420 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 237.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.189 85640 Z= 0.439 Angle : 1.308 23.986 125161 Z= 0.888 Chirality : 0.103 1.418 15716 Planarity : 0.009 0.467 8655 Dihedral : 25.570 179.853 45253 Min Nonbonded Distance : 0.713 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 4.56 % Allowed : 11.18 % Favored : 84.25 % Rotamer: Outliers : 9.44 % Allowed : 12.53 % Favored : 78.03 % Cbeta Deviations : 0.93 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.57 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.10), residues: 4776 helix: 0.51 (0.10), residues: 1513 sheet: -2.60 (0.16), residues: 795 loop : -3.66 (0.10), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 195 HIS 0.008 0.002 HIS T 93 PHE 0.025 0.002 PHE G 145 TYR 0.049 0.002 TYR G 208 ARG 0.012 0.001 ARG a 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1801 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 1413 time to evaluate : 4.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7153 (mptt) cc_final: 0.6938 (tppt) REVERT: A 38 TYR cc_start: 0.8473 (t80) cc_final: 0.7483 (t80) REVERT: A 120 LEU cc_start: 0.8925 (tm) cc_final: 0.8683 (tt) REVERT: A 138 TYR cc_start: 0.8233 (m-80) cc_final: 0.8014 (m-10) REVERT: A 139 VAL cc_start: 0.8699 (m) cc_final: 0.8282 (p) REVERT: A 204 TYR cc_start: 0.7593 (t80) cc_final: 0.7328 (t80) REVERT: B 38 PHE cc_start: 0.8029 (m-80) cc_final: 0.7816 (m-10) REVERT: B 48 VAL cc_start: 0.7584 (OUTLIER) cc_final: 0.7282 (p) REVERT: B 74 GLN cc_start: 0.8493 (mm-40) cc_final: 0.7953 (mm-40) REVERT: B 96 LEU cc_start: 0.4800 (OUTLIER) cc_final: 0.4561 (pp) REVERT: B 98 THR cc_start: 0.4588 (p) cc_final: 0.3698 (t) REVERT: B 99 ASN cc_start: 0.2137 (OUTLIER) cc_final: -0.0073 (p0) REVERT: B 155 TYR cc_start: 0.8156 (m-10) cc_final: 0.7178 (m-10) REVERT: B 189 ILE cc_start: 0.6474 (mp) cc_final: 0.6230 (mt) REVERT: B 204 ILE cc_start: 0.8769 (mt) cc_final: 0.8491 (mt) REVERT: C 48 ARG cc_start: 0.8150 (mtt90) cc_final: 0.7947 (ttm110) REVERT: C 76 GLN cc_start: 0.7679 (tp-100) cc_final: 0.7391 (tp40) REVERT: C 89 LYS cc_start: 0.7079 (mttp) cc_final: 0.6718 (mtmm) REVERT: C 96 ARG cc_start: 0.6980 (ptp90) cc_final: 0.6770 (ttt-90) REVERT: C 104 LYS cc_start: 0.9189 (ttmt) cc_final: 0.8404 (tttp) REVERT: C 179 ARG cc_start: 0.7380 (mtt-85) cc_final: 0.7178 (ttm110) REVERT: C 181 SER cc_start: 0.8690 (p) cc_final: 0.8222 (t) REVERT: C 217 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8079 (ttmm) REVERT: D 9 ARG cc_start: 0.8520 (ttm110) cc_final: 0.6972 (ttt180) REVERT: D 49 ILE cc_start: 0.7057 (mt) cc_final: 0.6716 (mp) REVERT: D 51 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6438 (mmt180) REVERT: D 61 GLU cc_start: 0.6312 (mp0) cc_final: 0.5983 (mm-30) REVERT: D 64 ARG cc_start: 0.5166 (ttm170) cc_final: 0.4725 (ttt180) REVERT: D 80 LYS cc_start: 0.5528 (mptt) cc_final: 0.4995 (ptpp) REVERT: D 90 ARG cc_start: 0.7900 (mtt180) cc_final: 0.6754 (ptm160) REVERT: D 96 LEU cc_start: 0.8519 (mt) cc_final: 0.8092 (mm) REVERT: D 135 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: D 173 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7546 (mmt-90) REVERT: E 6 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7057 (tttm) REVERT: E 111 VAL cc_start: 0.8789 (t) cc_final: 0.8585 (p) REVERT: E 155 LYS cc_start: 0.8263 (mttt) cc_final: 0.8051 (mtpt) REVERT: E 208 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8403 (m) REVERT: F 51 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6554 (pm20) REVERT: F 146 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7485 (mt-10) REVERT: F 173 SER cc_start: 0.8031 (OUTLIER) cc_final: 0.7557 (p) REVERT: F 186 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7589 (m-80) REVERT: F 187 ARG cc_start: 0.7742 (mpt180) cc_final: 0.7101 (mtt90) REVERT: F 188 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8060 (m-40) REVERT: F 210 SER cc_start: 0.5895 (OUTLIER) cc_final: 0.5401 (t) REVERT: G 1 MET cc_start: 0.4284 (mmm) cc_final: 0.3739 (mpp) REVERT: G 36 VAL cc_start: 0.4810 (OUTLIER) cc_final: 0.4198 (t) REVERT: G 93 LYS cc_start: 0.7483 (tmtt) cc_final: 0.7229 (tttp) REVERT: G 120 GLU cc_start: 0.5475 (mp0) cc_final: 0.5206 (mm-30) REVERT: G 178 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7202 (mt) REVERT: G 182 GLN cc_start: 0.5885 (OUTLIER) cc_final: 0.5396 (tm-30) REVERT: G 196 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7861 (ttmt) REVERT: H 28 GLU cc_start: 0.6435 (mt-10) cc_final: 0.6223 (mt-10) REVERT: H 48 GLU cc_start: 0.5606 (tp30) cc_final: 0.5155 (tm-30) REVERT: H 147 ASN cc_start: 0.8496 (m-40) cc_final: 0.8106 (m-40) REVERT: H 161 HIS cc_start: 0.7205 (m-70) cc_final: 0.6878 (m90) REVERT: H 165 LYS cc_start: 0.7889 (mttt) cc_final: 0.7302 (mtmt) REVERT: H 180 GLN cc_start: 0.8110 (mp10) cc_final: 0.7575 (mm-40) REVERT: I 96 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7973 (tm) REVERT: I 160 GLN cc_start: 0.3139 (OUTLIER) cc_final: 0.2753 (mp10) REVERT: I 170 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7141 (mp) REVERT: J 16 LYS cc_start: 0.8084 (mttt) cc_final: 0.7820 (ttmm) REVERT: J 42 ILE cc_start: 0.8312 (mt) cc_final: 0.8010 (mt) REVERT: J 68 LYS cc_start: 0.7259 (mttt) cc_final: 0.6658 (tttp) REVERT: J 83 ILE cc_start: 0.8262 (tt) cc_final: 0.8022 (tt) REVERT: J 115 LYS cc_start: 0.8378 (mttt) cc_final: 0.7967 (mptt) REVERT: J 126 ARG cc_start: 0.6575 (OUTLIER) cc_final: 0.5545 (ttt180) REVERT: K 54 PHE cc_start: 0.5167 (m-10) cc_final: 0.4875 (m-80) REVERT: L 10 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6568 (mp0) REVERT: L 56 LYS cc_start: 0.8586 (mmtm) cc_final: 0.8249 (mtmm) REVERT: L 70 ILE cc_start: 0.9416 (mp) cc_final: 0.9134 (mt) REVERT: L 87 ARG cc_start: 0.8530 (tmt-80) cc_final: 0.8250 (tmt170) REVERT: L 104 HIS cc_start: 0.8316 (t-90) cc_final: 0.7941 (t70) REVERT: L 136 ARG cc_start: 0.8346 (mpt-90) cc_final: 0.8081 (mpt-90) REVERT: M 79 LEU cc_start: 0.5338 (mt) cc_final: 0.5120 (mt) REVERT: M 80 ILE cc_start: 0.6236 (OUTLIER) cc_final: 0.5777 (mp) REVERT: M 104 ARG cc_start: 0.5758 (OUTLIER) cc_final: 0.4633 (ptm-80) REVERT: M 105 LYS cc_start: 0.1593 (OUTLIER) cc_final: 0.1156 (mmtm) REVERT: N 3 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7981 (mmp80) REVERT: N 142 GLU cc_start: 0.4543 (OUTLIER) cc_final: 0.2928 (mt-10) REVERT: O 25 ASP cc_start: 0.9209 (t70) cc_final: 0.8945 (t0) REVERT: P 17 TYR cc_start: 0.3074 (OUTLIER) cc_final: 0.2604 (t80) REVERT: P 21 ASP cc_start: 0.4754 (OUTLIER) cc_final: 0.4546 (p0) REVERT: P 38 PRO cc_start: 0.5862 (Cg_exo) cc_final: 0.5598 (Cg_endo) REVERT: P 52 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6116 (ptpt) REVERT: P 84 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7278 (tp) REVERT: P 127 ARG cc_start: 0.3600 (OUTLIER) cc_final: 0.2567 (mtm180) REVERT: Q 64 ASP cc_start: 0.6437 (m-30) cc_final: 0.6094 (m-30) REVERT: Q 94 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6954 (tt0) REVERT: Q 96 PHE cc_start: 0.7888 (m-80) cc_final: 0.7581 (m-80) REVERT: R 24 LEU cc_start: 0.8463 (mt) cc_final: 0.8262 (mt) REVERT: R 61 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.7054 (mp) REVERT: R 99 VAL cc_start: 0.7238 (m) cc_final: 0.7017 (m) REVERT: R 106 THR cc_start: 0.8748 (m) cc_final: 0.8496 (p) REVERT: S 45 LEU cc_start: 0.7663 (tt) cc_final: 0.7289 (tt) REVERT: S 49 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6711 (mmtp) REVERT: S 53 ASP cc_start: 0.7049 (m-30) cc_final: 0.5986 (t0) REVERT: S 74 GLN cc_start: 0.6250 (OUTLIER) cc_final: 0.5032 (mp10) REVERT: S 88 ARG cc_start: 0.6882 (tpp-160) cc_final: 0.6361 (mmm160) REVERT: S 98 TYR cc_start: 0.5893 (t80) cc_final: 0.5361 (t80) REVERT: T 68 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6920 (mtt-85) REVERT: T 70 GLN cc_start: 0.7348 (pt0) cc_final: 0.7103 (pm20) REVERT: T 102 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.5917 (ttp80) REVERT: T 115 GLU cc_start: 0.7891 (tt0) cc_final: 0.7182 (mm-30) REVERT: T 124 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.7119 (tt) REVERT: T 125 SER cc_start: 0.7604 (m) cc_final: 0.7153 (p) REVERT: U 69 LYS cc_start: 0.9016 (mttt) cc_final: 0.8784 (mttp) REVERT: U 84 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7425 (tpt) REVERT: V 25 LYS cc_start: 0.8836 (mttt) cc_final: 0.8088 (mtmm) REVERT: V 75 GLN cc_start: 0.8139 (mt0) cc_final: 0.7937 (tp40) REVERT: V 85 TYR cc_start: 0.8356 (t80) cc_final: 0.7994 (t80) REVERT: W 15 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7659 (t0) REVERT: W 18 GLU cc_start: 0.7149 (tp30) cc_final: 0.6792 (tp30) REVERT: W 25 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8322 (m) REVERT: W 28 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6836 (mmm-85) REVERT: W 81 VAL cc_start: 0.8904 (t) cc_final: 0.8679 (t) REVERT: W 101 TYR cc_start: 0.8516 (m-80) cc_final: 0.7716 (m-80) REVERT: W 118 ARG cc_start: 0.8629 (mtm180) cc_final: 0.8425 (mtp180) REVERT: X 23 ARG cc_start: 0.8464 (mmt90) cc_final: 0.8172 (tpp80) REVERT: X 38 PHE cc_start: 0.7739 (m-80) cc_final: 0.7465 (m-80) REVERT: X 109 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7491 (mtp180) REVERT: X 128 SER cc_start: 0.8530 (p) cc_final: 0.8143 (t) REVERT: Y 29 HIS cc_start: 0.6822 (OUTLIER) cc_final: 0.5921 (m-70) REVERT: Y 68 LYS cc_start: 0.8047 (tttt) cc_final: 0.7268 (tttp) REVERT: Y 98 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6544 (pt0) REVERT: Z 49 ARG cc_start: 0.6175 (OUTLIER) cc_final: 0.5412 (ttp80) REVERT: a 1 MET cc_start: 0.5694 (OUTLIER) cc_final: 0.4494 (mtm) REVERT: a 27 SER cc_start: 0.9047 (m) cc_final: 0.8834 (m) REVERT: a 37 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8358 (mttm) REVERT: a 38 ARG cc_start: 0.7817 (ttt180) cc_final: 0.7024 (mpt180) REVERT: b 65 THR cc_start: 0.8541 (p) cc_final: 0.8076 (p) REVERT: c 56 LEU cc_start: 0.7044 (pt) cc_final: 0.6776 (pt) REVERT: d 13 LYS cc_start: 0.8458 (mttt) cc_final: 0.8099 (mtpp) REVERT: d 16 LYS cc_start: 0.7154 (mmtt) cc_final: 0.6945 (mmtm) REVERT: d 40 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7421 (ptt-90) REVERT: d 52 PHE cc_start: 0.8209 (m-80) cc_final: 0.8003 (m-10) REVERT: e 10 ARG cc_start: 0.6147 (mmt180) cc_final: 0.5786 (ptm160) REVERT: f 94 LYS cc_start: 0.4871 (mmmt) cc_final: 0.4264 (mptt) REVERT: g 43 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8596 (tt) REVERT: g 93 TRP cc_start: 0.8745 (m100) cc_final: 0.8417 (m100) REVERT: g 99 ASN cc_start: 0.5792 (OUTLIER) cc_final: 0.5259 (m-40) REVERT: g 110 ASP cc_start: 0.7812 (p0) cc_final: 0.7253 (p0) REVERT: g 135 TRP cc_start: 0.7218 (m100) cc_final: 0.6879 (m100) REVERT: g 146 LEU cc_start: 0.8241 (mp) cc_final: 0.7542 (tp) REVERT: g 152 VAL cc_start: 0.8314 (t) cc_final: 0.7939 (p) REVERT: g 273 GLU cc_start: 0.4760 (OUTLIER) cc_final: 0.4436 (mt-10) outliers start: 388 outliers final: 73 residues processed: 1654 average time/residue: 0.8823 time to fit residues: 2338.6705 Evaluate side-chains 975 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 853 time to evaluate : 4.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 186 PHE Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 182 GLN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 160 GLN Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 8 TYR Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 126 ARG Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 104 ARG Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain N residue 3 ARG Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 89 TYR Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 52 LYS Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 127 ARG Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 100 SER Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 53 TRP Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain T residue 102 ARG Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 84 MET Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 50 TYR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 15 ASN Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 28 ARG Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 70 ASN Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 63 GLN Chi-restraints excluded: chain X residue 64 PRO Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 109 ARG Chi-restraints excluded: chain Y residue 29 HIS Chi-restraints excluded: chain Y residue 98 GLU Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 37 LYS Chi-restraints excluded: chain d residue 21 CYS Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 67 HIS Chi-restraints excluded: chain g residue 83 SER Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 273 GLU Chi-restraints excluded: chain g residue 315 ASN Chi-restraints excluded: chain g residue 321 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 563 optimal weight: 9.9990 chunk 505 optimal weight: 10.0000 chunk 280 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 341 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 chunk 522 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 317 optimal weight: 8.9990 chunk 389 optimal weight: 10.0000 chunk 605 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 92 HIS A 109 ASN A 131 GLN B 99 ASN B 101 HIS B 118 GLN B 211 HIS B 220 GLN C 64 HIS C 225 ASN D 92 HIS ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 HIS E 50 ASN E 130 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN E 224 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 202 ASN G 4 ASN G 190 GLN G 210 GLN H 71 HIS H 160 GLN H 170 GLN I 9 HIS I 53 GLN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 HIS ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 HIS ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 HIS ** L 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN N 21 ASN N 49 GLN N 58 HIS N 123 HIS ** N 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 GLN Q 83 GLN R 56 HIS S 12 GLN S 75 ASN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN T 48 GLN T 85 ASN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 HIS V 74 GLN V 81 ASN W 92 ASN W 117 HIS X 18 HIS X 75 GLN Y 22 GLN ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 82 HIS a 8 ASN f 104 ASN f 133 HIS g 32 ASN g 70 GLN g 79 ASN g 231 ASN ** g 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.183 85640 Z= 0.460 Angle : 1.040 17.533 125161 Z= 0.517 Chirality : 0.054 0.406 15716 Planarity : 0.009 0.165 8655 Dihedral : 25.651 179.655 35931 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 1.84 % Allowed : 9.99 % Favored : 88.17 % Rotamer: Outliers : 8.66 % Allowed : 19.10 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.09 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.12), residues: 4776 helix: 1.56 (0.13), residues: 1515 sheet: -2.13 (0.16), residues: 824 loop : -3.38 (0.10), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP S 84 HIS 0.014 0.003 HIS I 9 PHE 0.044 0.003 PHE D 24 TYR 0.030 0.003 TYR G 48 ARG 0.015 0.001 ARG J 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 980 time to evaluate : 4.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 SER cc_start: 0.8184 (p) cc_final: 0.7584 (m) REVERT: A 172 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8202 (tt) REVERT: A 200 ASP cc_start: 0.8202 (t70) cc_final: 0.7961 (t0) REVERT: A 204 TYR cc_start: 0.8658 (t80) cc_final: 0.8224 (t80) REVERT: B 99 ASN cc_start: 0.3281 (OUTLIER) cc_final: 0.2970 (m-40) REVERT: B 212 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.6155 (mp) REVERT: C 54 LYS cc_start: 0.8959 (mttt) cc_final: 0.8645 (mttm) REVERT: C 83 ASP cc_start: 0.7789 (p0) cc_final: 0.7575 (p0) REVERT: C 99 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: C 104 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8424 (ttmm) REVERT: C 179 ARG cc_start: 0.7662 (mtt-85) cc_final: 0.7108 (ttm110) REVERT: D 20 GLU cc_start: 0.7227 (tt0) cc_final: 0.6948 (tt0) REVERT: D 24 PHE cc_start: 0.5904 (m-80) cc_final: 0.5517 (m-80) REVERT: D 61 GLU cc_start: 0.6725 (mp0) cc_final: 0.6116 (mm-30) REVERT: D 64 ARG cc_start: 0.5590 (ttm170) cc_final: 0.4739 (ttt180) REVERT: D 75 LYS cc_start: 0.8252 (mptt) cc_final: 0.7838 (mmtm) REVERT: D 90 ARG cc_start: 0.7912 (mtt180) cc_final: 0.6775 (ptm160) REVERT: D 92 HIS cc_start: 0.6946 (OUTLIER) cc_final: 0.6459 (m90) REVERT: D 188 ILE cc_start: 0.9221 (mp) cc_final: 0.8792 (mm) REVERT: E 104 ASP cc_start: 0.8314 (t70) cc_final: 0.7977 (t70) REVERT: E 111 VAL cc_start: 0.8731 (t) cc_final: 0.8473 (p) REVERT: E 250 GLU cc_start: 0.7817 (tt0) cc_final: 0.7578 (tp30) REVERT: F 54 GLU cc_start: 0.6811 (mp0) cc_final: 0.6369 (mp0) REVERT: F 65 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7027 (tm-30) REVERT: F 114 ARG cc_start: 0.7993 (tpp-160) cc_final: 0.7682 (tpp-160) REVERT: F 121 GLU cc_start: 0.8033 (tp30) cc_final: 0.7669 (tp30) REVERT: F 167 LEU cc_start: 0.8627 (tp) cc_final: 0.8413 (tp) REVERT: F 188 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.7806 (m-40) REVERT: F 192 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7474 (pp) REVERT: F 220 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8069 (mm-30) REVERT: G 1 MET cc_start: 0.5107 (mmm) cc_final: 0.4572 (mmm) REVERT: G 4 ASN cc_start: 0.7553 (t0) cc_final: 0.7152 (t0) REVERT: G 12 THR cc_start: 0.7581 (p) cc_final: 0.7368 (p) REVERT: G 16 ILE cc_start: 0.5839 (OUTLIER) cc_final: 0.5467 (pt) REVERT: G 17 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6946 (tp30) REVERT: G 56 ASN cc_start: 0.7092 (t0) cc_final: 0.6742 (t0) REVERT: G 196 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8110 (mttp) REVERT: H 27 LEU cc_start: 0.7817 (tp) cc_final: 0.7441 (tp) REVERT: H 33 GLU cc_start: 0.6205 (tm-30) cc_final: 0.5984 (tm-30) REVERT: H 50 GLU cc_start: 0.8381 (tp30) cc_final: 0.8095 (tp30) REVERT: H 88 ARG cc_start: 0.6777 (mtt180) cc_final: 0.6175 (mtm180) REVERT: H 91 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8379 (mp) REVERT: H 114 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7073 (mtt90) REVERT: H 152 ILE cc_start: 0.9245 (mp) cc_final: 0.8914 (mm) REVERT: H 165 LYS cc_start: 0.7861 (mttt) cc_final: 0.7512 (mtmm) REVERT: I 61 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6189 (tt0) REVERT: I 77 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6495 (ptp90) REVERT: I 160 GLN cc_start: 0.3739 (OUTLIER) cc_final: 0.3519 (mt0) REVERT: J 7 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8402 (m) REVERT: J 11 THR cc_start: 0.6364 (OUTLIER) cc_final: 0.6072 (t) REVERT: J 62 ARG cc_start: 0.7153 (ptp-170) cc_final: 0.6843 (ptm160) REVERT: J 68 LYS cc_start: 0.7454 (mttt) cc_final: 0.7122 (tptm) REVERT: J 83 ILE cc_start: 0.8675 (tt) cc_final: 0.8463 (tt) REVERT: J 93 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8187 (tt) REVERT: J 115 LYS cc_start: 0.8730 (mttt) cc_final: 0.8192 (mmtp) REVERT: K 5 LYS cc_start: 0.7052 (tptm) cc_final: 0.6807 (mmmt) REVERT: K 61 TRP cc_start: 0.8028 (m100) cc_final: 0.7589 (m-10) REVERT: K 77 ARG cc_start: 0.6959 (mtt90) cc_final: 0.6653 (mtt90) REVERT: K 84 GLU cc_start: 0.5737 (mm-30) cc_final: 0.5432 (mm-30) REVERT: K 86 ILE cc_start: 0.3734 (OUTLIER) cc_final: 0.3336 (mt) REVERT: M 18 GLU cc_start: 0.4108 (pt0) cc_final: 0.3894 (tt0) REVERT: M 104 ARG cc_start: 0.5834 (OUTLIER) cc_final: 0.4898 (ptm-80) REVERT: N 52 VAL cc_start: 0.8188 (t) cc_final: 0.7776 (p) REVERT: N 53 LEU cc_start: 0.9019 (tp) cc_final: 0.8799 (tp) REVERT: O 53 ASP cc_start: 0.7922 (m-30) cc_final: 0.7698 (m-30) REVERT: O 82 LYS cc_start: 0.8653 (mttt) cc_final: 0.8398 (mtpp) REVERT: O 125 SER cc_start: 0.5978 (t) cc_final: 0.5747 (p) REVERT: P 127 ARG cc_start: 0.3050 (OUTLIER) cc_final: 0.2031 (mtm180) REVERT: Q 94 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7749 (tm-30) REVERT: R 6 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8622 (p) REVERT: R 105 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8202 (mm-40) REVERT: R 106 THR cc_start: 0.8911 (m) cc_final: 0.8469 (p) REVERT: R 121 VAL cc_start: 0.6718 (t) cc_final: 0.6516 (t) REVERT: S 45 LEU cc_start: 0.7622 (tt) cc_final: 0.7112 (tt) REVERT: S 49 LYS cc_start: 0.7243 (tptt) cc_final: 0.6867 (mmtp) REVERT: S 57 ARG cc_start: 0.6454 (mmm160) cc_final: 0.5874 (ttp-170) REVERT: S 88 ARG cc_start: 0.7186 (tpp-160) cc_final: 0.6766 (mmm160) REVERT: T 68 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7575 (mtt-85) REVERT: T 69 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7714 (mmtt) REVERT: T 102 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7316 (ttp80) REVERT: T 115 GLU cc_start: 0.7958 (tt0) cc_final: 0.7226 (mm-30) REVERT: T 125 SER cc_start: 0.7648 (m) cc_final: 0.7313 (p) REVERT: U 56 VAL cc_start: 0.7931 (t) cc_final: 0.7344 (m) REVERT: V 25 LYS cc_start: 0.8996 (mttt) cc_final: 0.8272 (mtmm) REVERT: W 15 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.7633 (t0) REVERT: W 20 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8499 (m) REVERT: W 28 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7108 (mmm-85) REVERT: X 30 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8428 (ttmm) REVERT: X 63 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7309 (tp40) REVERT: X 109 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7719 (mmm160) REVERT: X 136 TRP cc_start: 0.8285 (t60) cc_final: 0.8006 (t60) REVERT: Y 68 LYS cc_start: 0.8403 (tttt) cc_final: 0.7988 (tttp) REVERT: Y 98 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7192 (pt0) REVERT: a 1 MET cc_start: 0.6091 (OUTLIER) cc_final: 0.5509 (mtp) REVERT: a 39 MET cc_start: 0.8669 (tpp) cc_final: 0.8265 (ttm) REVERT: a 45 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8274 (p) REVERT: b 1 MET cc_start: 0.2928 (mmm) cc_final: 0.2672 (tpt) REVERT: b 42 ASN cc_start: 0.5439 (m-40) cc_final: 0.4755 (p0) REVERT: c 11 LYS cc_start: 0.6708 (tmmt) cc_final: 0.6479 (tttp) REVERT: c 32 PHE cc_start: 0.5726 (OUTLIER) cc_final: 0.4274 (p90) REVERT: c 35 ASP cc_start: 0.7532 (t0) cc_final: 0.6978 (t0) REVERT: c 38 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7828 (ttp80) REVERT: c 61 ARG cc_start: 0.5757 (mtm-85) cc_final: 0.5471 (mmt-90) REVERT: d 13 LYS cc_start: 0.8603 (mttt) cc_final: 0.8177 (mtpp) REVERT: d 21 CYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7665 (p) REVERT: d 54 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7651 (ttmm) REVERT: e 46 ASN cc_start: 0.8154 (t0) cc_final: 0.7945 (m-40) REVERT: g 93 TRP cc_start: 0.8741 (m100) cc_final: 0.8479 (m100) REVERT: g 99 ASN cc_start: 0.6683 (OUTLIER) cc_final: 0.6005 (m-40) REVERT: g 134 VAL cc_start: 0.8271 (t) cc_final: 0.7741 (p) REVERT: g 135 TRP cc_start: 0.7550 (m100) cc_final: 0.7027 (m100) REVERT: g 146 LEU cc_start: 0.7844 (mp) cc_final: 0.7128 (tp) REVERT: g 152 VAL cc_start: 0.8726 (t) cc_final: 0.8499 (p) REVERT: g 194 ARG cc_start: 0.8290 (mtt180) cc_final: 0.7543 (mmp-170) REVERT: g 210 GLN cc_start: 0.6569 (OUTLIER) cc_final: 0.6339 (tp-100) REVERT: g 230 TRP cc_start: 0.6119 (m100) cc_final: 0.5754 (m100) REVERT: g 273 GLU cc_start: 0.5066 (OUTLIER) cc_final: 0.4695 (mt-10) REVERT: g 293 ASP cc_start: 0.8006 (m-30) cc_final: 0.6361 (p0) outliers start: 356 outliers final: 174 residues processed: 1233 average time/residue: 0.7981 time to fit residues: 1644.6862 Evaluate side-chains 1030 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 820 time to evaluate : 4.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 104 ARG Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 186 PHE Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 114 ARG Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 160 GLN Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 126 ARG Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 104 ARG Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 52 LYS Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 127 ARG Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 85 ILE Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 75 ASN Chi-restraints excluded: chain S residue 87 ASN Chi-restraints excluded: chain S residue 92 VAL Chi-restraints excluded: chain T residue 29 GLU Chi-restraints excluded: chain T residue 33 TYR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 53 TRP Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain T residue 102 ARG Chi-restraints excluded: chain T residue 107 SER Chi-restraints excluded: chain T residue 127 ASN Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 50 TYR Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 74 GLN Chi-restraints excluded: chain V residue 80 LYS Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 5 SER Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 15 ASN Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 28 ARG Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 70 ASN Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 30 LYS Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain X residue 57 ILE Chi-restraints excluded: chain X residue 63 GLN Chi-restraints excluded: chain X residue 109 ARG Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 98 GLU Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 8 ASN Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 37 LYS Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 82 ARG Chi-restraints excluded: chain b residue 41 LEU Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 48 VAL Chi-restraints excluded: chain d residue 21 CYS Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 54 LYS Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain f residue 99 LYS Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain f residue 142 CYS Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 67 HIS Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 176 SER Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 210 GLN Chi-restraints excluded: chain g residue 273 GLU Chi-restraints excluded: chain g residue 278 ILE Chi-restraints excluded: chain g residue 297 VAL Chi-restraints excluded: chain g residue 315 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 336 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 504 optimal weight: 10.0000 chunk 412 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 606 optimal weight: 10.0000 chunk 655 optimal weight: 40.0000 chunk 540 optimal weight: 40.0000 chunk 601 optimal weight: 8.9990 chunk 206 optimal weight: 20.0000 chunk 486 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 148 ASN B 209 ASN D 159 HIS E 8 HIS ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 ASN ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 160 GLN K 47 GLN L 37 ASN L 104 HIS ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN N 151 ASN O 12 GLN O 24 ASN ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 ASN V 74 GLN X 18 HIS X 79 ASN Y 107 GLN ** b 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 123 ASN g 79 ASN g 292 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.142 85640 Z= 0.416 Angle : 0.905 16.214 125161 Z= 0.459 Chirality : 0.049 0.305 15716 Planarity : 0.008 0.147 8655 Dihedral : 25.401 179.998 35822 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 1.80 % Allowed : 11.68 % Favored : 86.52 % Rotamer: Outliers : 8.76 % Allowed : 21.95 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.09 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.12), residues: 4776 helix: 1.19 (0.13), residues: 1515 sheet: -1.90 (0.17), residues: 810 loop : -3.28 (0.11), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP g 151 HIS 0.058 0.002 HIS D 92 PHE 0.042 0.003 PHE D 24 TYR 0.049 0.003 TYR V 85 ARG 0.041 0.001 ARG E 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 874 time to evaluate : 4.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.8187 (m-40) cc_final: 0.7895 (m110) REVERT: A 71 GLU cc_start: 0.7502 (pp20) cc_final: 0.7213 (pp20) REVERT: A 78 SER cc_start: 0.8053 (p) cc_final: 0.7678 (m) REVERT: A 198 MET cc_start: 0.7305 (ttp) cc_final: 0.6959 (ttp) REVERT: A 200 ASP cc_start: 0.8345 (t70) cc_final: 0.8097 (t0) REVERT: A 204 TYR cc_start: 0.8802 (t80) cc_final: 0.8279 (t80) REVERT: B 47 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6508 (pt) REVERT: B 117 TRP cc_start: 0.7164 (m-10) cc_final: 0.6884 (m-10) REVERT: B 219 LYS cc_start: 0.6135 (tppt) cc_final: 0.5780 (mtpp) REVERT: C 99 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: D 20 GLU cc_start: 0.7437 (tt0) cc_final: 0.6997 (tt0) REVERT: D 24 PHE cc_start: 0.5969 (m-10) cc_final: 0.5717 (m-80) REVERT: D 31 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8651 (mm-30) REVERT: D 61 GLU cc_start: 0.6927 (mp0) cc_final: 0.6429 (mm-30) REVERT: D 64 ARG cc_start: 0.6356 (ttm170) cc_final: 0.5414 (ttt180) REVERT: D 90 ARG cc_start: 0.7774 (mtt180) cc_final: 0.6786 (ptm160) REVERT: D 91 VAL cc_start: 0.6656 (OUTLIER) cc_final: 0.6398 (m) REVERT: D 92 HIS cc_start: 0.6902 (m-70) cc_final: 0.6440 (t-90) REVERT: D 105 MET cc_start: 0.8312 (tpp) cc_final: 0.7214 (tpp) REVERT: D 187 LYS cc_start: 0.8803 (mttt) cc_final: 0.7836 (mtpp) REVERT: D 189 MET cc_start: 0.7941 (tpt) cc_final: 0.7687 (tpt) REVERT: E 104 ASP cc_start: 0.8404 (t70) cc_final: 0.7969 (t70) REVERT: E 105 VAL cc_start: 0.8912 (m) cc_final: 0.8597 (t) REVERT: E 151 ASP cc_start: 0.8021 (t0) cc_final: 0.7755 (t0) REVERT: F 26 GLU cc_start: 0.5781 (mm-30) cc_final: 0.5318 (mp0) REVERT: F 51 GLU cc_start: 0.7439 (tt0) cc_final: 0.6941 (pt0) REVERT: F 68 LYS cc_start: 0.7830 (mttm) cc_final: 0.7097 (tptp) REVERT: F 114 ARG cc_start: 0.7881 (tpp-160) cc_final: 0.7172 (tpp-160) REVERT: F 130 ASN cc_start: 0.8734 (t0) cc_final: 0.8533 (t0) REVERT: F 168 ARG cc_start: 0.8302 (ttt90) cc_final: 0.8093 (tpt-90) REVERT: G 1 MET cc_start: 0.5423 (mmm) cc_final: 0.5015 (mmm) REVERT: G 4 ASN cc_start: 0.7946 (t0) cc_final: 0.7371 (t0) REVERT: G 16 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5933 (pt) REVERT: G 17 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7317 (tp30) REVERT: G 96 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8298 (p) REVERT: G 125 THR cc_start: 0.4899 (OUTLIER) cc_final: 0.4541 (p) REVERT: G 145 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: G 164 LYS cc_start: 0.2158 (OUTLIER) cc_final: 0.1909 (mmtt) REVERT: G 196 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8195 (mttp) REVERT: H 71 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6126 (m-70) REVERT: H 147 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.7947 (m110) REVERT: H 165 LYS cc_start: 0.8087 (mttt) cc_final: 0.7835 (mtmm) REVERT: I 61 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6558 (tt0) REVERT: I 77 ARG cc_start: 0.7518 (ptp-110) cc_final: 0.7140 (ttm110) REVERT: I 161 PHE cc_start: 0.6419 (m-80) cc_final: 0.5977 (m-10) REVERT: J 7 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8144 (m) REVERT: J 11 THR cc_start: 0.7052 (OUTLIER) cc_final: 0.6851 (t) REVERT: J 68 LYS cc_start: 0.7430 (mttt) cc_final: 0.7106 (tttp) REVERT: J 72 GLU cc_start: 0.5897 (mp0) cc_final: 0.5606 (mp0) REVERT: J 115 LYS cc_start: 0.8925 (mttt) cc_final: 0.8386 (mmtp) REVERT: J 145 SER cc_start: 0.8448 (m) cc_final: 0.7955 (p) REVERT: J 168 ARG cc_start: 0.6760 (mtt180) cc_final: 0.6421 (mtt-85) REVERT: K 61 TRP cc_start: 0.8265 (m100) cc_final: 0.8036 (m-10) REVERT: K 66 TYR cc_start: 0.8679 (m-80) cc_final: 0.8456 (m-10) REVERT: K 75 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.5100 (m-80) REVERT: K 77 ARG cc_start: 0.7016 (mtt90) cc_final: 0.6752 (mtt90) REVERT: K 84 GLU cc_start: 0.5928 (mm-30) cc_final: 0.5703 (mm-30) REVERT: L 47 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.8146 (t) REVERT: L 140 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8723 (mp) REVERT: M 104 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.5343 (ptt90) REVERT: N 99 ARG cc_start: 0.6517 (mtp85) cc_final: 0.6099 (mmm-85) REVERT: P 28 MET cc_start: 0.7806 (mmm) cc_final: 0.6235 (ptm) REVERT: P 127 ARG cc_start: 0.3819 (OUTLIER) cc_final: 0.2983 (mtm180) REVERT: Q 42 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7779 (tm-30) REVERT: R 6 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8704 (p) REVERT: R 62 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7542 (tm-30) REVERT: R 105 GLN cc_start: 0.8381 (mm-40) cc_final: 0.7997 (mp10) REVERT: R 106 THR cc_start: 0.8775 (m) cc_final: 0.8379 (p) REVERT: S 49 LYS cc_start: 0.7457 (tptt) cc_final: 0.7144 (mmtp) REVERT: S 137 HIS cc_start: 0.5792 (OUTLIER) cc_final: 0.5574 (m90) REVERT: T 17 ASN cc_start: 0.7732 (m110) cc_final: 0.7447 (m110) REVERT: T 48 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.6919 (mt0) REVERT: T 69 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7655 (mtmt) REVERT: T 115 GLU cc_start: 0.8309 (tt0) cc_final: 0.7463 (mm-30) REVERT: T 116 ILE cc_start: 0.8369 (mm) cc_final: 0.8058 (mm) REVERT: U 32 LYS cc_start: 0.8394 (mmtt) cc_final: 0.8008 (mtmm) REVERT: U 48 PHE cc_start: 0.6643 (m-10) cc_final: 0.6441 (m-10) REVERT: U 92 ASP cc_start: 0.6459 (OUTLIER) cc_final: 0.6232 (m-30) REVERT: V 2 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7850 (mm-30) REVERT: V 40 ASP cc_start: 0.6245 (OUTLIER) cc_final: 0.6014 (p0) REVERT: V 74 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7196 (tt0) REVERT: V 85 TYR cc_start: 0.8270 (t80) cc_final: 0.8055 (t80) REVERT: W 15 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.7958 (t0) REVERT: W 20 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8559 (m) REVERT: W 28 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7071 (mmm-85) REVERT: W 115 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7989 (mt-10) REVERT: X 30 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8317 (tttt) REVERT: X 109 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7790 (mmm160) REVERT: Y 68 LYS cc_start: 0.8438 (tttt) cc_final: 0.8068 (tttp) REVERT: Y 98 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7340 (pt0) REVERT: Z 92 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7723 (t) REVERT: a 1 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5656 (mtp) REVERT: a 5 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8224 (mpt-90) REVERT: a 32 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8261 (ttpp) REVERT: a 45 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8037 (p) REVERT: b 36 LYS cc_start: 0.7049 (tttt) cc_final: 0.6818 (mtpt) REVERT: b 57 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6640 (pp20) REVERT: c 11 LYS cc_start: 0.7020 (tmmt) cc_final: 0.6802 (tttp) REVERT: c 29 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7800 (ttm-80) REVERT: c 31 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7113 (mt-10) REVERT: c 32 PHE cc_start: 0.6026 (OUTLIER) cc_final: 0.4431 (p90) REVERT: c 35 ASP cc_start: 0.7527 (t0) cc_final: 0.6987 (t0) REVERT: d 13 LYS cc_start: 0.8638 (mttt) cc_final: 0.8139 (mtpp) REVERT: d 21 CYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7969 (p) REVERT: d 54 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7831 (ttmm) REVERT: f 121 CYS cc_start: 0.4943 (OUTLIER) cc_final: 0.3768 (p) REVERT: g 11 ARG cc_start: 0.7412 (ttm170) cc_final: 0.7026 (ttp-110) REVERT: g 79 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.6922 (m-40) REVERT: g 99 ASN cc_start: 0.6601 (OUTLIER) cc_final: 0.5848 (m110) REVERT: g 134 VAL cc_start: 0.8523 (t) cc_final: 0.8163 (p) REVERT: g 135 TRP cc_start: 0.7881 (m100) cc_final: 0.7570 (m100) REVERT: g 146 LEU cc_start: 0.7738 (mp) cc_final: 0.7066 (tp) REVERT: g 194 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7247 (mmp-170) REVERT: g 199 PHE cc_start: 0.7254 (m-80) cc_final: 0.6968 (m-10) REVERT: g 210 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6808 (tp-100) REVERT: g 223 LYS cc_start: 0.6227 (mtmm) cc_final: 0.5628 (mtmm) REVERT: g 239 MET cc_start: 0.5326 (OUTLIER) cc_final: 0.4576 (mmm) REVERT: g 272 LEU cc_start: 0.5001 (mt) cc_final: 0.4631 (mt) REVERT: g 273 GLU cc_start: 0.5370 (OUTLIER) cc_final: 0.5167 (mt-10) outliers start: 360 outliers final: 222 residues processed: 1116 average time/residue: 0.7863 time to fit residues: 1469.1215 Evaluate side-chains 1039 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 773 time to evaluate : 4.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain H residue 29 ASN Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 126 ARG Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 104 ARG Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 103 ARG Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 52 LYS Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 127 ARG Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 87 ASN Chi-restraints excluded: chain S residue 137 HIS Chi-restraints excluded: chain T residue 29 GLU Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 53 TRP Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 107 SER Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain T residue 127 ASN Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 50 TYR Chi-restraints excluded: chain V residue 71 ARG Chi-restraints excluded: chain V residue 74 GLN Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 5 SER Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 15 ASN Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 28 ARG Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 70 ASN Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 30 LYS Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain X residue 63 GLN Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 109 ARG Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 98 GLU Chi-restraints excluded: chain Y residue 125 ILE Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 92 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 5 ARG Chi-restraints excluded: chain a residue 8 ASN Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 32 LYS Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 37 LYS Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 94 ILE Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 57 GLU Chi-restraints excluded: chain b residue 64 CYS Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 48 VAL Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain d residue 21 CYS Chi-restraints excluded: chain d residue 54 LYS Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 99 LYS Chi-restraints excluded: chain f residue 106 TYR Chi-restraints excluded: chain f residue 121 CYS Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain f residue 142 CYS Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 67 HIS Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 79 ASN Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 100 SER Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain g residue 176 SER Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 210 GLN Chi-restraints excluded: chain g residue 214 ASP Chi-restraints excluded: chain g residue 239 MET Chi-restraints excluded: chain g residue 273 GLU Chi-restraints excluded: chain g residue 292 GLN Chi-restraints excluded: chain g residue 297 VAL Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain g residue 315 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 599 optimal weight: 10.0000 chunk 456 optimal weight: 20.0000 chunk 314 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 289 optimal weight: 10.0000 chunk 407 optimal weight: 7.9990 chunk 608 optimal weight: 10.0000 chunk 644 optimal weight: 10.0000 chunk 318 optimal weight: 7.9990 chunk 577 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 overall best weight: 7.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN B 56 ASN B 92 GLN D 92 HIS ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 ASN G 182 GLN H 42 GLN ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN I 53 GLN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN L 14 GLN ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 HIS ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 HIS V 74 GLN W 44 HIS X 18 HIS X 89 ASN a 8 ASN b 5 GLN c 27 GLN g 51 ASN g 79 ASN g 231 ASN g 292 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.6526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.140 85640 Z= 0.487 Angle : 0.964 16.189 125161 Z= 0.482 Chirality : 0.050 0.335 15716 Planarity : 0.008 0.149 8655 Dihedral : 25.332 179.714 35801 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 1.63 % Allowed : 11.62 % Favored : 86.75 % Rotamer: Outliers : 9.95 % Allowed : 23.92 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.09 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.11), residues: 4776 helix: 0.64 (0.13), residues: 1523 sheet: -1.73 (0.17), residues: 833 loop : -3.35 (0.11), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP g 151 HIS 0.021 0.002 HIS D 92 PHE 0.034 0.003 PHE B 138 TYR 0.033 0.003 TYR g 80 ARG 0.014 0.001 ARG J 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1275 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 409 poor density : 866 time to evaluate : 4.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6967 (m-30) REVERT: A 69 ASN cc_start: 0.7814 (m-40) cc_final: 0.7593 (m110) REVERT: A 79 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6987 (ttm-80) REVERT: A 200 ASP cc_start: 0.8502 (t70) cc_final: 0.8275 (t0) REVERT: A 204 TYR cc_start: 0.8780 (t80) cc_final: 0.8388 (t80) REVERT: B 47 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6712 (pt) REVERT: B 176 VAL cc_start: 0.7489 (t) cc_final: 0.7190 (p) REVERT: B 181 LEU cc_start: 0.5022 (OUTLIER) cc_final: 0.4677 (tp) REVERT: B 183 GLN cc_start: 0.7064 (mt0) cc_final: 0.6460 (mt0) REVERT: B 223 PHE cc_start: 0.8316 (m-80) cc_final: 0.7910 (p90) REVERT: C 135 ILE cc_start: 0.8781 (mt) cc_final: 0.8507 (tt) REVERT: C 250 ASP cc_start: 0.8811 (p0) cc_final: 0.8258 (p0) REVERT: D 61 GLU cc_start: 0.7098 (mp0) cc_final: 0.6326 (mm-30) REVERT: D 64 ARG cc_start: 0.6209 (ttm170) cc_final: 0.5305 (ttt180) REVERT: D 90 ARG cc_start: 0.7719 (mtt180) cc_final: 0.6772 (ptm160) REVERT: D 92 HIS cc_start: 0.7100 (m90) cc_final: 0.6810 (t-90) REVERT: D 168 ILE cc_start: 0.8994 (mp) cc_final: 0.8727 (tt) REVERT: D 179 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7803 (pt0) REVERT: D 187 LYS cc_start: 0.8742 (mttt) cc_final: 0.7967 (mtpp) REVERT: D 204 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6857 (p0) REVERT: E 105 VAL cc_start: 0.8763 (m) cc_final: 0.8512 (t) REVERT: E 162 VAL cc_start: 0.9306 (t) cc_final: 0.9060 (m) REVERT: F 45 PHE cc_start: 0.8065 (t80) cc_final: 0.7736 (t80) REVERT: F 68 LYS cc_start: 0.8025 (mttm) cc_final: 0.7382 (tptm) REVERT: F 99 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7942 (mt) REVERT: F 114 ARG cc_start: 0.8056 (tpp-160) cc_final: 0.7396 (tpp-160) REVERT: F 192 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.7135 (mt) REVERT: G 4 ASN cc_start: 0.8102 (t0) cc_final: 0.7356 (t0) REVERT: G 16 ILE cc_start: 0.6183 (OUTLIER) cc_final: 0.5969 (pt) REVERT: G 17 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7479 (tp30) REVERT: G 35 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6626 (tp30) REVERT: G 96 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8141 (p) REVERT: G 125 THR cc_start: 0.5592 (OUTLIER) cc_final: 0.5275 (p) REVERT: G 145 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7469 (m-80) REVERT: G 196 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8313 (mttp) REVERT: H 7 LYS cc_start: 0.7314 (mmtt) cc_final: 0.6866 (mptt) REVERT: H 88 ARG cc_start: 0.7376 (mpt-90) cc_final: 0.7117 (mmt90) REVERT: H 147 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.7912 (m110) REVERT: H 165 LYS cc_start: 0.8811 (mttt) cc_final: 0.8312 (mtmm) REVERT: I 61 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7323 (tt0) REVERT: I 77 ARG cc_start: 0.7489 (ptp-110) cc_final: 0.7280 (ttm110) REVERT: I 161 PHE cc_start: 0.7473 (m-80) cc_final: 0.7141 (m-80) REVERT: I 170 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7339 (mp) REVERT: J 11 THR cc_start: 0.7169 (OUTLIER) cc_final: 0.6958 (t) REVERT: J 68 LYS cc_start: 0.7637 (mttt) cc_final: 0.7259 (tttm) REVERT: J 115 LYS cc_start: 0.8937 (mttt) cc_final: 0.8511 (mmtp) REVERT: J 145 SER cc_start: 0.8567 (m) cc_final: 0.8156 (p) REVERT: J 149 ARG cc_start: 0.7790 (tpt-90) cc_final: 0.7320 (tpt-90) REVERT: J 168 ARG cc_start: 0.6966 (mtt180) cc_final: 0.6730 (mtt-85) REVERT: K 66 TYR cc_start: 0.8717 (m-80) cc_final: 0.8458 (m-80) REVERT: K 70 GLU cc_start: 0.6018 (mt-10) cc_final: 0.5647 (mp0) REVERT: K 75 TYR cc_start: 0.6283 (OUTLIER) cc_final: 0.4923 (m-80) REVERT: K 77 ARG cc_start: 0.7093 (mtt90) cc_final: 0.6790 (mtt90) REVERT: K 84 GLU cc_start: 0.5877 (mm-30) cc_final: 0.5608 (mm-30) REVERT: K 86 ILE cc_start: 0.3893 (OUTLIER) cc_final: 0.3248 (mt) REVERT: L 32 LYS cc_start: 0.7868 (tppt) cc_final: 0.7097 (ttpt) REVERT: L 47 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8293 (t) REVERT: M 104 ARG cc_start: 0.5656 (OUTLIER) cc_final: 0.5224 (ptt90) REVERT: N 99 ARG cc_start: 0.7036 (mtp85) cc_final: 0.6664 (mmm-85) REVERT: O 53 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7752 (t0) REVERT: O 82 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8689 (mtpp) REVERT: P 28 MET cc_start: 0.7683 (mmm) cc_final: 0.5797 (ptm) REVERT: P 84 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7454 (tp) REVERT: P 89 MET cc_start: 0.7752 (pmm) cc_final: 0.7455 (pmm) REVERT: P 127 ARG cc_start: 0.3964 (OUTLIER) cc_final: 0.3156 (mtm180) REVERT: Q 42 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7837 (tm-30) REVERT: R 6 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8875 (p) REVERT: R 62 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7562 (tm-30) REVERT: R 105 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8217 (mp10) REVERT: S 11 PHE cc_start: 0.5112 (OUTLIER) cc_final: 0.4661 (m-10) REVERT: S 12 GLN cc_start: 0.6702 (tm-30) cc_final: 0.6493 (tm-30) REVERT: S 49 LYS cc_start: 0.7537 (tptt) cc_final: 0.7087 (mmtp) REVERT: S 88 ARG cc_start: 0.7173 (tpp-160) cc_final: 0.6947 (mtp85) REVERT: S 128 PHE cc_start: 0.3724 (OUTLIER) cc_final: 0.3384 (t80) REVERT: S 143 ARG cc_start: 0.5801 (mtm110) cc_final: 0.5507 (mtm-85) REVERT: T 25 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7378 (mm-40) REVERT: T 69 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7795 (mtmt) REVERT: T 115 GLU cc_start: 0.8156 (tt0) cc_final: 0.7518 (mm-30) REVERT: U 32 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8100 (mtmm) REVERT: U 92 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6479 (m-30) REVERT: V 2 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7793 (mm-30) REVERT: V 40 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6624 (p0) REVERT: W 15 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8091 (t0) REVERT: W 20 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8653 (m) REVERT: W 28 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7144 (mmm-85) REVERT: X 30 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8503 (tttt) REVERT: X 109 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7888 (mmm160) REVERT: X 137 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8424 (mmmm) REVERT: Y 8 ARG cc_start: 0.8000 (mtt90) cc_final: 0.7581 (mtm180) REVERT: Y 18 LEU cc_start: 0.8677 (mt) cc_final: 0.8424 (mp) REVERT: Y 68 LYS cc_start: 0.8499 (tttt) cc_final: 0.8127 (tttp) REVERT: Y 98 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7413 (pt0) REVERT: a 5 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8221 (mpt-90) REVERT: a 32 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8494 (ttpp) REVERT: b 41 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7109 (tt) REVERT: c 31 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7129 (mt-10) REVERT: c 32 PHE cc_start: 0.5854 (OUTLIER) cc_final: 0.4382 (p90) REVERT: c 35 ASP cc_start: 0.7644 (t0) cc_final: 0.7116 (t0) REVERT: d 13 LYS cc_start: 0.8642 (mttt) cc_final: 0.8102 (mtpp) REVERT: d 54 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7873 (ttmm) REVERT: e 42 ARG cc_start: 0.8785 (ttm170) cc_final: 0.8392 (mtm180) REVERT: g 55 PHE cc_start: 0.6034 (OUTLIER) cc_final: 0.5383 (t80) REVERT: g 73 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7580 (m) REVERT: g 79 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7191 (m-40) REVERT: g 99 ASN cc_start: 0.6875 (OUTLIER) cc_final: 0.5999 (m110) REVERT: g 135 TRP cc_start: 0.7800 (m100) cc_final: 0.7473 (m100) REVERT: g 146 LEU cc_start: 0.7591 (mp) cc_final: 0.6966 (tp) REVERT: g 179 MET cc_start: 0.6723 (mmm) cc_final: 0.6059 (mtm) REVERT: g 194 ARG cc_start: 0.8202 (mtt180) cc_final: 0.7505 (mmp-170) REVERT: g 210 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6736 (tp-100) REVERT: g 239 MET cc_start: 0.4978 (OUTLIER) cc_final: 0.4354 (mmm) REVERT: g 257 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6469 (t80) REVERT: g 272 LEU cc_start: 0.5156 (mt) cc_final: 0.4048 (mt) REVERT: g 273 GLU cc_start: 0.4347 (OUTLIER) cc_final: 0.3747 (mt-10) outliers start: 409 outliers final: 260 residues processed: 1140 average time/residue: 0.7699 time to fit residues: 1487.8669 Evaluate side-chains 1098 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 792 time to evaluate : 4.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain H residue 29 ASN Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 65 PHE Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 74 ARG Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 126 ARG Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 28 ASN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 116 ARG Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 104 ARG Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 18 TYR Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 103 ARG Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 123 TYR Chi-restraints excluded: chain P residue 127 ARG Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 87 ASN Chi-restraints excluded: chain S residue 128 PHE Chi-restraints excluded: chain T residue 29 GLU Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 53 TRP Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 97 SER Chi-restraints excluded: chain T residue 107 SER Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 127 ASN Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 85 ARG Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 71 ARG Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 5 SER Chi-restraints excluded: chain W residue 15 ASN Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 28 ARG Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 70 ASN Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 30 LYS Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 109 ARG Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 13 ILE Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 98 GLU Chi-restraints excluded: chain a residue 5 ARG Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 32 LYS Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 37 LYS Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 94 ILE Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 5 GLN Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 41 LEU Chi-restraints excluded: chain b residue 64 CYS Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 27 GLN Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 54 LYS Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 99 LYS Chi-restraints excluded: chain f residue 106 TYR Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 55 PHE Chi-restraints excluded: chain g residue 67 HIS Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 79 ASN Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 110 ASP Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 176 SER Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 203 ASN Chi-restraints excluded: chain g residue 210 GLN Chi-restraints excluded: chain g residue 231 ASN Chi-restraints excluded: chain g residue 239 MET Chi-restraints excluded: chain g residue 240 ASN Chi-restraints excluded: chain g residue 257 PHE Chi-restraints excluded: chain g residue 273 GLU Chi-restraints excluded: chain g residue 297 VAL Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain g residue 315 ASN Chi-restraints excluded: chain g residue 321 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 536 optimal weight: 30.0000 chunk 365 optimal weight: 0.0020 chunk 9 optimal weight: 10.0000 chunk 480 optimal weight: 7.9990 chunk 266 optimal weight: 6.9990 chunk 550 optimal weight: 30.0000 chunk 445 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 329 optimal weight: 9.9990 chunk 578 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 HIS B 92 GLN B 124 ASN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN L 110 HIS M 130 HIS ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 ASN U 98 HIS X 89 ASN ** Y 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN g 79 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 85640 Z= 0.307 Angle : 0.792 12.684 125161 Z= 0.401 Chirality : 0.043 0.305 15716 Planarity : 0.006 0.150 8655 Dihedral : 25.149 179.687 35782 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 1.65 % Allowed : 10.76 % Favored : 87.58 % Rotamer: Outliers : 8.66 % Allowed : 25.77 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.09 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.12), residues: 4776 helix: 1.01 (0.13), residues: 1514 sheet: -1.53 (0.18), residues: 818 loop : -3.21 (0.11), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP g 151 HIS 0.007 0.001 HIS T 64 PHE 0.045 0.002 PHE S 85 TYR 0.025 0.002 TYR S 30 ARG 0.010 0.001 ARG a 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 850 time to evaluate : 4.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.8103 (m-40) cc_final: 0.7795 (m110) REVERT: A 79 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6932 (ttm-80) REVERT: A 200 ASP cc_start: 0.8466 (t70) cc_final: 0.8138 (t0) REVERT: A 204 TYR cc_start: 0.8685 (t80) cc_final: 0.8260 (t80) REVERT: B 47 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6826 (pp) REVERT: B 90 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6697 (tm-30) REVERT: B 181 LEU cc_start: 0.5006 (OUTLIER) cc_final: 0.4644 (tp) REVERT: B 193 ILE cc_start: 0.7792 (mt) cc_final: 0.7584 (mt) REVERT: B 223 PHE cc_start: 0.8296 (m-80) cc_final: 0.7961 (t80) REVERT: C 193 MET cc_start: 0.8604 (mmp) cc_final: 0.8379 (mmp) REVERT: C 227 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.5458 (t80) REVERT: D 61 GLU cc_start: 0.7000 (mp0) cc_final: 0.6357 (mm-30) REVERT: D 64 ARG cc_start: 0.6221 (ttm170) cc_final: 0.5597 (ttt180) REVERT: D 90 ARG cc_start: 0.7776 (mtt180) cc_final: 0.6787 (ptm160) REVERT: D 91 VAL cc_start: 0.6482 (OUTLIER) cc_final: 0.6174 (m) REVERT: D 92 HIS cc_start: 0.7418 (m90) cc_final: 0.6888 (t70) REVERT: D 105 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7645 (tpp) REVERT: D 143 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6769 (ttp80) REVERT: D 187 LYS cc_start: 0.8597 (mttt) cc_final: 0.8050 (mtpp) REVERT: E 6 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7227 (mtpt) REVERT: E 87 MET cc_start: 0.8490 (mtp) cc_final: 0.8269 (ttm) REVERT: E 162 VAL cc_start: 0.9306 (t) cc_final: 0.9093 (m) REVERT: F 68 LYS cc_start: 0.8135 (mttm) cc_final: 0.7423 (tptm) REVERT: F 92 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8217 (t) REVERT: F 114 ARG cc_start: 0.7955 (tpp-160) cc_final: 0.7286 (tpp-160) REVERT: F 168 ARG cc_start: 0.8368 (ttt90) cc_final: 0.8079 (tpt-90) REVERT: F 187 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7897 (mtt180) REVERT: F 192 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.7027 (mt) REVERT: G 4 ASN cc_start: 0.8016 (t0) cc_final: 0.7321 (t0) REVERT: G 17 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7063 (tp30) REVERT: G 39 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.5227 (mm-30) REVERT: G 64 LYS cc_start: 0.8685 (tptm) cc_final: 0.8286 (tttm) REVERT: G 96 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8205 (p) REVERT: G 145 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: G 196 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8214 (mttp) REVERT: H 7 LYS cc_start: 0.7327 (mmtt) cc_final: 0.6825 (mptt) REVERT: H 71 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6104 (m-70) REVERT: H 88 ARG cc_start: 0.7383 (mpt-90) cc_final: 0.7060 (mmt90) REVERT: H 118 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8145 (tp) REVERT: H 165 LYS cc_start: 0.8766 (mttt) cc_final: 0.8150 (mtmm) REVERT: I 61 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7540 (tt0) REVERT: I 170 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7403 (mp) REVERT: J 11 THR cc_start: 0.6430 (OUTLIER) cc_final: 0.6226 (t) REVERT: J 37 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7466 (ttmm) REVERT: J 68 LYS cc_start: 0.7511 (mttt) cc_final: 0.7235 (tttp) REVERT: J 110 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6294 (mt0) REVERT: J 115 LYS cc_start: 0.8794 (mttt) cc_final: 0.8458 (mmtm) REVERT: J 126 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.5882 (tpt-90) REVERT: J 138 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7383 (mtmm) REVERT: J 145 SER cc_start: 0.8309 (m) cc_final: 0.7807 (p) REVERT: J 168 ARG cc_start: 0.7041 (mtt180) cc_final: 0.6830 (mtt-85) REVERT: K 70 GLU cc_start: 0.6006 (mt-10) cc_final: 0.5627 (mp0) REVERT: K 75 TYR cc_start: 0.6026 (OUTLIER) cc_final: 0.4917 (m-80) REVERT: K 76 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6515 (tt) REVERT: K 77 ARG cc_start: 0.7019 (mtt90) cc_final: 0.6643 (mtt90) REVERT: K 84 GLU cc_start: 0.5875 (mm-30) cc_final: 0.5581 (mm-30) REVERT: L 32 LYS cc_start: 0.7755 (tppt) cc_final: 0.7097 (ttpt) REVERT: L 47 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8265 (t) REVERT: L 116 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7174 (mmm-85) REVERT: L 140 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8794 (mp) REVERT: M 104 ARG cc_start: 0.5630 (OUTLIER) cc_final: 0.5234 (ptt90) REVERT: N 18 TYR cc_start: 0.6318 (OUTLIER) cc_final: 0.5096 (p90) REVERT: N 62 GLN cc_start: 0.8746 (mp10) cc_final: 0.8363 (mp10) REVERT: N 99 ARG cc_start: 0.6977 (mtp85) cc_final: 0.6680 (mmm-85) REVERT: O 105 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8128 (tt) REVERT: P 28 MET cc_start: 0.7619 (mmm) cc_final: 0.6092 (ptm) REVERT: P 84 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7781 (tp) REVERT: P 127 ARG cc_start: 0.3693 (OUTLIER) cc_final: 0.3167 (mtm180) REVERT: Q 42 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8031 (tm-30) REVERT: R 18 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6780 (mm-30) REVERT: R 105 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8095 (mp10) REVERT: R 106 THR cc_start: 0.8649 (m) cc_final: 0.8446 (p) REVERT: S 11 PHE cc_start: 0.5227 (OUTLIER) cc_final: 0.4966 (m-10) REVERT: S 85 PHE cc_start: 0.7076 (t80) cc_final: 0.6850 (t80) REVERT: S 88 ARG cc_start: 0.7163 (tpp-160) cc_final: 0.6854 (mtp85) REVERT: S 128 PHE cc_start: 0.3644 (OUTLIER) cc_final: 0.3298 (t80) REVERT: T 25 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7350 (mm-40) REVERT: T 48 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.6900 (mt0) REVERT: T 97 SER cc_start: 0.7757 (OUTLIER) cc_final: 0.7277 (p) REVERT: T 115 GLU cc_start: 0.8139 (tt0) cc_final: 0.7498 (mm-30) REVERT: U 32 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8109 (mtmm) REVERT: V 2 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7755 (mm-30) REVERT: W 15 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.7931 (t0) REVERT: W 20 THR cc_start: 0.8909 (p) cc_final: 0.8583 (m) REVERT: W 54 ASP cc_start: 0.8632 (t70) cc_final: 0.8174 (t0) REVERT: X 30 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8460 (tttt) REVERT: X 109 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7422 (mmm160) REVERT: X 137 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8312 (mmmm) REVERT: Y 8 ARG cc_start: 0.8340 (mtt90) cc_final: 0.7898 (mtm110) REVERT: Y 18 LEU cc_start: 0.8503 (mt) cc_final: 0.8284 (mp) REVERT: Y 68 LYS cc_start: 0.8435 (tttt) cc_final: 0.8150 (tttp) REVERT: Y 98 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: b 3 LEU cc_start: 0.7817 (mt) cc_final: 0.7615 (mp) REVERT: b 36 LYS cc_start: 0.7518 (tttt) cc_final: 0.7157 (tttp) REVERT: c 31 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7008 (mt-10) REVERT: c 32 PHE cc_start: 0.5834 (OUTLIER) cc_final: 0.4273 (p90) REVERT: c 35 ASP cc_start: 0.7500 (t0) cc_final: 0.7072 (t0) REVERT: c 38 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7791 (mtm110) REVERT: d 13 LYS cc_start: 0.8627 (mttt) cc_final: 0.8104 (mtpp) REVERT: d 54 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7762 (ttmm) REVERT: e 42 ARG cc_start: 0.8755 (ttm170) cc_final: 0.8401 (mtm-85) REVERT: f 89 LYS cc_start: 0.1648 (OUTLIER) cc_final: 0.1384 (tptp) REVERT: g 11 ARG cc_start: 0.7509 (ttm170) cc_final: 0.7123 (ttp-110) REVERT: g 99 ASN cc_start: 0.6622 (OUTLIER) cc_final: 0.5735 (m-40) REVERT: g 135 TRP cc_start: 0.7771 (m100) cc_final: 0.7497 (m100) REVERT: g 146 LEU cc_start: 0.7573 (mp) cc_final: 0.6897 (tp) REVERT: g 179 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6165 (mtm) REVERT: g 194 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7383 (mmp-170) REVERT: g 210 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6732 (tp-100) REVERT: g 235 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7960 (ptmt) REVERT: g 239 MET cc_start: 0.5487 (OUTLIER) cc_final: 0.4859 (mmm) REVERT: g 256 ARG cc_start: 0.7695 (ttt180) cc_final: 0.6873 (mpp-170) REVERT: g 257 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6067 (t80) REVERT: g 273 GLU cc_start: 0.5090 (OUTLIER) cc_final: 0.4208 (mp0) outliers start: 356 outliers final: 233 residues processed: 1098 average time/residue: 0.7710 time to fit residues: 1443.6594 Evaluate side-chains 1064 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 782 time to evaluate : 4.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 104 ARG Chi-restraints excluded: chain F residue 187 ARG Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 29 ASN Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 126 ARG Chi-restraints excluded: chain J residue 138 LYS Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 58 CYS Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 116 ARG Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 69 GLN Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 104 ARG Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 18 TYR Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 123 TYR Chi-restraints excluded: chain P residue 127 ARG Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 87 ASN Chi-restraints excluded: chain S residue 128 PHE Chi-restraints excluded: chain T residue 29 GLU Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 53 TRP Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 97 SER Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain T residue 127 ASN Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 50 TYR Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 15 ASN Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 70 ASN Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 30 LYS Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 109 ARG Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 98 GLU Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain a residue 8 ASN Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 37 LYS Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 94 ILE Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 41 LEU Chi-restraints excluded: chain b residue 64 CYS Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 48 VAL Chi-restraints excluded: chain d residue 54 LYS Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 89 LYS Chi-restraints excluded: chain f residue 99 LYS Chi-restraints excluded: chain f residue 106 TYR Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 67 HIS Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 176 SER Chi-restraints excluded: chain g residue 179 MET Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 210 GLN Chi-restraints excluded: chain g residue 214 ASP Chi-restraints excluded: chain g residue 239 MET Chi-restraints excluded: chain g residue 240 ASN Chi-restraints excluded: chain g residue 257 PHE Chi-restraints excluded: chain g residue 273 GLU Chi-restraints excluded: chain g residue 297 VAL Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain g residue 315 ASN Chi-restraints excluded: chain g residue 321 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 216 optimal weight: 0.9980 chunk 580 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 378 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 645 optimal weight: 10.0000 chunk 535 optimal weight: 40.0000 chunk 298 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 338 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN B 92 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 GLN I 139 ASN K 47 GLN ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN N 49 GLN ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 ASN U 98 HIS b 5 GLN g 210 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.7181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 85640 Z= 0.292 Angle : 0.770 21.240 125161 Z= 0.388 Chirality : 0.042 0.302 15716 Planarity : 0.006 0.150 8655 Dihedral : 25.014 179.969 35765 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 1.55 % Allowed : 11.08 % Favored : 87.37 % Rotamer: Outliers : 8.88 % Allowed : 25.50 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.09 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.12), residues: 4776 helix: 1.06 (0.13), residues: 1515 sheet: -1.45 (0.18), residues: 830 loop : -3.14 (0.11), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 61 HIS 0.007 0.001 HIS E 142 PHE 0.073 0.002 PHE D 24 TYR 0.026 0.002 TYR G 156 ARG 0.022 0.001 ARG V 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 826 time to evaluate : 4.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.8073 (m-40) cc_final: 0.7762 (m110) REVERT: A 71 GLU cc_start: 0.7555 (pp20) cc_final: 0.7152 (pp20) REVERT: A 200 ASP cc_start: 0.8422 (t70) cc_final: 0.8089 (t0) REVERT: A 204 TYR cc_start: 0.8670 (t80) cc_final: 0.8310 (t80) REVERT: B 47 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7058 (pt) REVERT: B 90 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6987 (tm-30) REVERT: B 119 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7381 (p) REVERT: B 148 ASN cc_start: 0.7648 (m110) cc_final: 0.7396 (t0) REVERT: B 212 ILE cc_start: 0.6383 (OUTLIER) cc_final: 0.5897 (tp) REVERT: B 223 PHE cc_start: 0.8170 (m-80) cc_final: 0.7722 (t80) REVERT: C 193 MET cc_start: 0.8468 (mmp) cc_final: 0.8232 (mmp) REVERT: C 227 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.5500 (t80) REVERT: D 24 PHE cc_start: 0.5490 (m-80) cc_final: 0.4720 (m-80) REVERT: D 34 TYR cc_start: 0.8743 (t80) cc_final: 0.8209 (t80) REVERT: D 61 GLU cc_start: 0.6996 (mp0) cc_final: 0.6282 (mm-30) REVERT: D 64 ARG cc_start: 0.6120 (ttm170) cc_final: 0.5572 (ttt180) REVERT: D 65 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7134 (mtp180) REVERT: D 90 ARG cc_start: 0.7878 (mtt180) cc_final: 0.6808 (ptm160) REVERT: D 91 VAL cc_start: 0.6476 (OUTLIER) cc_final: 0.6083 (m) REVERT: D 92 HIS cc_start: 0.7300 (m90) cc_final: 0.6760 (t70) REVERT: D 105 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7412 (tpp) REVERT: D 143 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6711 (ttp80) REVERT: D 187 LYS cc_start: 0.8671 (mttt) cc_final: 0.8098 (mtpp) REVERT: D 190 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7233 (ptpp) REVERT: E 40 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7343 (tm-30) REVERT: E 162 VAL cc_start: 0.9303 (t) cc_final: 0.9042 (m) REVERT: F 51 GLU cc_start: 0.7348 (tt0) cc_final: 0.7026 (tp30) REVERT: F 54 GLU cc_start: 0.6581 (mm-30) cc_final: 0.6349 (mm-30) REVERT: F 68 LYS cc_start: 0.7892 (mttm) cc_final: 0.7567 (tppt) REVERT: F 100 MET cc_start: 0.7953 (mtm) cc_final: 0.7695 (ptp) REVERT: F 192 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.7104 (mt) REVERT: G 4 ASN cc_start: 0.8095 (t0) cc_final: 0.7278 (t0) REVERT: G 17 GLU cc_start: 0.7554 (mt-10) cc_final: 0.6996 (tp30) REVERT: G 39 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6367 (mm-30) REVERT: G 64 LYS cc_start: 0.8714 (tptm) cc_final: 0.8363 (tttm) REVERT: G 96 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8209 (p) REVERT: G 125 THR cc_start: 0.5564 (OUTLIER) cc_final: 0.5222 (p) REVERT: G 145 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7131 (m-80) REVERT: G 196 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8208 (mttp) REVERT: H 7 LYS cc_start: 0.7252 (mmtt) cc_final: 0.6803 (mptt) REVERT: H 71 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.5970 (m-70) REVERT: H 88 ARG cc_start: 0.7514 (mpt-90) cc_final: 0.7135 (mmt90) REVERT: H 147 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.7765 (m110) REVERT: H 165 LYS cc_start: 0.8813 (mttt) cc_final: 0.8225 (mtmm) REVERT: I 103 GLN cc_start: 0.8086 (mt0) cc_final: 0.7842 (mt0) REVERT: I 161 PHE cc_start: 0.7412 (m-80) cc_final: 0.6873 (m-80) REVERT: I 170 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7249 (mp) REVERT: J 37 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7528 (ttmm) REVERT: J 68 LYS cc_start: 0.7482 (mttt) cc_final: 0.7151 (tttp) REVERT: J 115 LYS cc_start: 0.8765 (mttt) cc_final: 0.8423 (mmtm) REVERT: J 126 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6010 (ttt180) REVERT: J 138 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7335 (mtmm) REVERT: J 145 SER cc_start: 0.8331 (m) cc_final: 0.8078 (p) REVERT: J 168 ARG cc_start: 0.7018 (mtt180) cc_final: 0.6725 (mtt-85) REVERT: K 70 GLU cc_start: 0.5901 (mt-10) cc_final: 0.5398 (mp0) REVERT: K 71 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.5622 (mm-30) REVERT: K 75 TYR cc_start: 0.5955 (OUTLIER) cc_final: 0.4824 (m-80) REVERT: K 76 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6508 (tt) REVERT: K 77 ARG cc_start: 0.7019 (mtt90) cc_final: 0.6616 (mtt90) REVERT: K 84 GLU cc_start: 0.5851 (mm-30) cc_final: 0.5527 (mm-30) REVERT: L 32 LYS cc_start: 0.7938 (tppt) cc_final: 0.7198 (ttpt) REVERT: L 47 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8220 (t) REVERT: L 116 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7066 (mmm-85) REVERT: L 140 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8796 (mp) REVERT: M 104 ARG cc_start: 0.5663 (OUTLIER) cc_final: 0.5446 (ptt90) REVERT: N 18 TYR cc_start: 0.6352 (OUTLIER) cc_final: 0.5124 (p90) REVERT: N 62 GLN cc_start: 0.8702 (mp10) cc_final: 0.8357 (mp10) REVERT: N 99 ARG cc_start: 0.6941 (mtp85) cc_final: 0.6603 (mmm-85) REVERT: O 124 ASP cc_start: 0.6762 (t0) cc_final: 0.5979 (t0) REVERT: P 24 LYS cc_start: 0.6731 (mmpt) cc_final: 0.6147 (mmpt) REVERT: P 28 MET cc_start: 0.7635 (mmm) cc_final: 0.6141 (ptm) REVERT: P 108 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7657 (tpt-90) REVERT: P 127 ARG cc_start: 0.3607 (OUTLIER) cc_final: 0.3330 (mtm180) REVERT: Q 21 HIS cc_start: 0.7538 (m-70) cc_final: 0.6592 (m-70) REVERT: R 18 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6936 (mm-30) REVERT: R 106 THR cc_start: 0.8673 (m) cc_final: 0.8439 (p) REVERT: S 11 PHE cc_start: 0.5180 (OUTLIER) cc_final: 0.4878 (m-10) REVERT: S 21 ASN cc_start: 0.8287 (t0) cc_final: 0.7997 (t0) REVERT: S 85 PHE cc_start: 0.7007 (t80) cc_final: 0.6566 (t80) REVERT: S 88 ARG cc_start: 0.7103 (tpp-160) cc_final: 0.6860 (mtt-85) REVERT: S 128 PHE cc_start: 0.3666 (OUTLIER) cc_final: 0.3371 (t80) REVERT: T 25 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7350 (mm-40) REVERT: T 115 GLU cc_start: 0.8167 (tt0) cc_final: 0.7505 (mm-30) REVERT: U 27 THR cc_start: 0.7541 (OUTLIER) cc_final: 0.6998 (p) REVERT: U 32 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8102 (mtmm) REVERT: V 2 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7740 (mm-30) REVERT: V 34 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7996 (tp) REVERT: W 15 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.7901 (t0) REVERT: W 20 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8536 (m) REVERT: W 54 ASP cc_start: 0.8713 (t70) cc_final: 0.8279 (t0) REVERT: X 30 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8486 (tttt) REVERT: X 109 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7549 (mmm160) REVERT: X 137 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8243 (mmmm) REVERT: Y 18 LEU cc_start: 0.8507 (mt) cc_final: 0.8061 (mp) REVERT: Y 26 ASP cc_start: 0.8230 (t0) cc_final: 0.7934 (t0) REVERT: Y 68 LYS cc_start: 0.8333 (tttt) cc_final: 0.7920 (tttp) REVERT: Y 83 LYS cc_start: 0.7998 (tttp) cc_final: 0.7675 (mmtt) REVERT: Y 98 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7117 (pt0) REVERT: Y 99 LYS cc_start: 0.7131 (tptt) cc_final: 0.6796 (tttp) REVERT: Z 78 VAL cc_start: 0.7787 (t) cc_final: 0.7427 (p) REVERT: a 32 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8259 (ttpp) REVERT: a 50 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8217 (mt) REVERT: b 36 LYS cc_start: 0.7506 (tttt) cc_final: 0.7113 (tttp) REVERT: c 31 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6960 (mt-10) REVERT: c 32 PHE cc_start: 0.5803 (OUTLIER) cc_final: 0.4237 (p90) REVERT: c 35 ASP cc_start: 0.7597 (t0) cc_final: 0.7069 (t0) REVERT: d 13 LYS cc_start: 0.8702 (mttt) cc_final: 0.8145 (mtpp) REVERT: d 54 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7745 (ttmm) REVERT: g 46 TRP cc_start: 0.7591 (OUTLIER) cc_final: 0.7266 (m100) REVERT: g 73 VAL cc_start: 0.8056 (OUTLIER) cc_final: 0.7673 (m) REVERT: g 99 ASN cc_start: 0.6602 (OUTLIER) cc_final: 0.5663 (m-40) REVERT: g 135 TRP cc_start: 0.7785 (m100) cc_final: 0.7560 (m100) REVERT: g 146 LEU cc_start: 0.7502 (mp) cc_final: 0.6852 (tp) REVERT: g 179 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6382 (mmm) REVERT: g 194 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7288 (mmm160) REVERT: g 210 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6746 (tp-100) REVERT: g 239 MET cc_start: 0.5521 (OUTLIER) cc_final: 0.5001 (mmm) REVERT: g 256 ARG cc_start: 0.7375 (ttt180) cc_final: 0.6634 (mpp80) REVERT: g 257 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6129 (t80) REVERT: g 273 GLU cc_start: 0.4919 (OUTLIER) cc_final: 0.3959 (mp0) outliers start: 365 outliers final: 261 residues processed: 1075 average time/residue: 0.7609 time to fit residues: 1409.0846 Evaluate side-chains 1089 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 777 time to evaluate : 4.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 40 GLN Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 104 ARG Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain H residue 29 ASN Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 65 PHE Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 126 ARG Chi-restraints excluded: chain J residue 138 LYS Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain L residue 14 GLN Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 58 CYS Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 116 ARG Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 69 GLN Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 104 ARG Chi-restraints excluded: chain N residue 18 TYR Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain P residue 123 TYR Chi-restraints excluded: chain P residue 127 ARG Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 87 ASN Chi-restraints excluded: chain S residue 128 PHE Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 29 GLU Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 53 TRP Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 97 SER Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 127 ASN Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 33 GLN Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain V residue 50 TYR Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 GLN Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 15 ASN Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 70 ASN Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain W residue 99 PHE Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 30 LYS Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 109 ARG Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 13 ILE Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 98 GLU Chi-restraints excluded: chain a residue 8 ASN Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain a residue 32 LYS Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 37 LYS Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 94 ILE Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 5 GLN Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 56 CYS Chi-restraints excluded: chain b residue 64 CYS Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 48 VAL Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 54 LYS Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 99 LYS Chi-restraints excluded: chain f residue 106 TYR Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 46 TRP Chi-restraints excluded: chain g residue 67 HIS Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 100 SER Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 176 SER Chi-restraints excluded: chain g residue 179 MET Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 203 ASN Chi-restraints excluded: chain g residue 210 GLN Chi-restraints excluded: chain g residue 239 MET Chi-restraints excluded: chain g residue 240 ASN Chi-restraints excluded: chain g residue 245 ASP Chi-restraints excluded: chain g residue 257 PHE Chi-restraints excluded: chain g residue 273 GLU Chi-restraints excluded: chain g residue 297 VAL Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain g residue 315 ASN Chi-restraints excluded: chain g residue 316 VAL Chi-restraints excluded: chain g residue 321 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 622 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 367 optimal weight: 6.9990 chunk 471 optimal weight: 8.9990 chunk 365 optimal weight: 0.5980 chunk 543 optimal weight: 9.9990 chunk 360 optimal weight: 0.6980 chunk 642 optimal weight: 20.0000 chunk 402 optimal weight: 0.0000 chunk 391 optimal weight: 9.9990 chunk 296 optimal weight: 4.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 137 HIS U 98 HIS c 27 GLN g 210 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.7390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 85640 Z= 0.231 Angle : 0.721 20.523 125161 Z= 0.363 Chirality : 0.039 0.282 15716 Planarity : 0.006 0.147 8655 Dihedral : 24.897 179.831 35755 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 1.53 % Allowed : 10.28 % Favored : 88.19 % Rotamer: Outliers : 7.49 % Allowed : 27.52 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.09 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.12), residues: 4776 helix: 1.26 (0.13), residues: 1512 sheet: -1.39 (0.17), residues: 837 loop : -3.05 (0.11), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP g 46 HIS 0.007 0.001 HIS Z 95 PHE 0.052 0.002 PHE D 24 TYR 0.026 0.002 TYR G 156 ARG 0.011 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 835 time to evaluate : 4.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7472 (pp20) cc_final: 0.7087 (pp20) REVERT: A 200 ASP cc_start: 0.8461 (t70) cc_final: 0.8025 (t0) REVERT: A 204 TYR cc_start: 0.8687 (t80) cc_final: 0.8400 (t80) REVERT: B 47 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6844 (pp) REVERT: B 62 LYS cc_start: 0.7127 (pttt) cc_final: 0.6684 (tptt) REVERT: B 90 GLU cc_start: 0.6864 (tm-30) cc_final: 0.6488 (tm-30) REVERT: B 119 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7396 (p) REVERT: B 148 ASN cc_start: 0.7861 (m110) cc_final: 0.7525 (t0) REVERT: B 223 PHE cc_start: 0.8158 (m-80) cc_final: 0.7665 (t80) REVERT: C 124 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7820 (pttp) REVERT: C 193 MET cc_start: 0.8536 (mmp) cc_final: 0.8189 (mmp) REVERT: D 24 PHE cc_start: 0.5441 (m-80) cc_final: 0.4534 (m-80) REVERT: D 61 GLU cc_start: 0.6840 (mp0) cc_final: 0.6367 (mm-30) REVERT: D 64 ARG cc_start: 0.5932 (ttm170) cc_final: 0.5590 (ttt180) REVERT: D 65 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7106 (mtp180) REVERT: D 90 ARG cc_start: 0.7888 (mtt180) cc_final: 0.6806 (ptm160) REVERT: D 91 VAL cc_start: 0.6916 (OUTLIER) cc_final: 0.6653 (m) REVERT: D 92 HIS cc_start: 0.7309 (m90) cc_final: 0.6757 (t70) REVERT: D 105 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7468 (tpp) REVERT: D 143 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6678 (ttp80) REVERT: D 187 LYS cc_start: 0.8589 (mttt) cc_final: 0.8177 (mtpp) REVERT: D 190 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7123 (ptpp) REVERT: E 6 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.7031 (mtpt) REVERT: E 40 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7278 (tm-30) REVERT: E 162 VAL cc_start: 0.9314 (t) cc_final: 0.9058 (m) REVERT: F 51 GLU cc_start: 0.7344 (tt0) cc_final: 0.7071 (tp30) REVERT: F 92 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8120 (t) REVERT: F 100 MET cc_start: 0.8009 (mtm) cc_final: 0.7774 (ptp) REVERT: F 192 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7054 (mt) REVERT: F 227 ARG cc_start: 0.6013 (mtp85) cc_final: 0.5454 (mtp85) REVERT: G 4 ASN cc_start: 0.8007 (t0) cc_final: 0.7241 (t0) REVERT: G 39 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6226 (mm-30) REVERT: G 64 LYS cc_start: 0.8675 (tptm) cc_final: 0.8365 (tttm) REVERT: G 96 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8225 (p) REVERT: G 119 GLN cc_start: 0.5829 (mp10) cc_final: 0.4975 (pm20) REVERT: G 125 THR cc_start: 0.5421 (OUTLIER) cc_final: 0.5132 (p) REVERT: G 145 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: G 196 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8166 (mttp) REVERT: H 7 LYS cc_start: 0.7254 (mmtt) cc_final: 0.6786 (mptt) REVERT: H 71 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.5921 (m-70) REVERT: H 88 ARG cc_start: 0.7500 (mpt-90) cc_final: 0.7148 (mmt90) REVERT: H 147 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.7745 (m110) REVERT: H 165 LYS cc_start: 0.8826 (mttt) cc_final: 0.8238 (mtmm) REVERT: I 84 HIS cc_start: 0.8468 (t70) cc_final: 0.8035 (t-90) REVERT: I 103 GLN cc_start: 0.8028 (mt0) cc_final: 0.7784 (mt0) REVERT: I 158 ASP cc_start: 0.7102 (m-30) cc_final: 0.6840 (m-30) REVERT: I 161 PHE cc_start: 0.7522 (m-80) cc_final: 0.7144 (m-80) REVERT: I 170 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7221 (mp) REVERT: J 37 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7437 (ttmm) REVERT: J 68 LYS cc_start: 0.7718 (mttt) cc_final: 0.7238 (tttm) REVERT: J 115 LYS cc_start: 0.8666 (mttt) cc_final: 0.8311 (mmtm) REVERT: J 138 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7330 (mtmm) REVERT: J 145 SER cc_start: 0.8280 (m) cc_final: 0.7973 (p) REVERT: K 70 GLU cc_start: 0.5887 (mt-10) cc_final: 0.5632 (mt-10) REVERT: K 71 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.5504 (mm-30) REVERT: K 75 TYR cc_start: 0.5925 (OUTLIER) cc_final: 0.4804 (m-80) REVERT: K 76 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6541 (tt) REVERT: K 77 ARG cc_start: 0.7016 (mtt90) cc_final: 0.6551 (mtt90) REVERT: K 84 GLU cc_start: 0.5721 (mm-30) cc_final: 0.5504 (mm-30) REVERT: L 32 LYS cc_start: 0.7863 (tppt) cc_final: 0.7186 (ttpt) REVERT: L 47 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8205 (t) REVERT: N 62 GLN cc_start: 0.8680 (mp10) cc_final: 0.8334 (mp10) REVERT: N 99 ARG cc_start: 0.6936 (mtp85) cc_final: 0.6665 (mmm-85) REVERT: O 124 ASP cc_start: 0.6555 (t0) cc_final: 0.6006 (t0) REVERT: P 24 LYS cc_start: 0.6569 (mmpt) cc_final: 0.5937 (mmpt) REVERT: P 28 MET cc_start: 0.7728 (mmm) cc_final: 0.6493 (ptm) REVERT: P 108 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7650 (tpt-90) REVERT: P 127 ARG cc_start: 0.3472 (OUTLIER) cc_final: 0.3267 (mtm180) REVERT: Q 21 HIS cc_start: 0.7488 (m-70) cc_final: 0.6559 (m-70) REVERT: R 18 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6987 (mm-30) REVERT: R 62 GLN cc_start: 0.7846 (tm-30) cc_final: 0.7608 (tm-30) REVERT: R 105 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7542 (mp10) REVERT: R 106 THR cc_start: 0.8684 (m) cc_final: 0.8420 (p) REVERT: S 11 PHE cc_start: 0.5035 (OUTLIER) cc_final: 0.4793 (m-10) REVERT: S 21 ASN cc_start: 0.8134 (t0) cc_final: 0.7867 (t0) REVERT: S 128 PHE cc_start: 0.3992 (OUTLIER) cc_final: 0.3758 (t80) REVERT: T 24 ARG cc_start: 0.6854 (mmm-85) cc_final: 0.6490 (tpp80) REVERT: T 48 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.6743 (mt0) REVERT: T 97 SER cc_start: 0.7721 (OUTLIER) cc_final: 0.7249 (p) REVERT: T 115 GLU cc_start: 0.8151 (tt0) cc_final: 0.7475 (mm-30) REVERT: U 32 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8128 (mtmm) REVERT: V 2 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7706 (mm-30) REVERT: V 3 ASN cc_start: 0.6428 (t0) cc_final: 0.6220 (t0) REVERT: V 34 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8033 (tp) REVERT: W 15 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.7841 (t0) REVERT: W 20 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8523 (m) REVERT: W 54 ASP cc_start: 0.8666 (t70) cc_final: 0.8255 (t0) REVERT: X 30 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8446 (tttt) REVERT: X 137 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8263 (mmmm) REVERT: Y 8 ARG cc_start: 0.8193 (mtt90) cc_final: 0.7843 (mtm110) REVERT: Y 18 LEU cc_start: 0.8449 (mt) cc_final: 0.8063 (mt) REVERT: Y 68 LYS cc_start: 0.8274 (tttt) cc_final: 0.8000 (tttp) REVERT: Y 83 LYS cc_start: 0.8232 (tttp) cc_final: 0.8006 (mttm) REVERT: Y 98 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7112 (pt0) REVERT: Y 99 LYS cc_start: 0.7068 (tptt) cc_final: 0.6729 (tttp) REVERT: Z 78 VAL cc_start: 0.7832 (t) cc_final: 0.7458 (p) REVERT: a 32 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8237 (ttpp) REVERT: b 36 LYS cc_start: 0.7514 (tttt) cc_final: 0.7214 (tttp) REVERT: c 31 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6877 (mt-10) REVERT: c 32 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.4206 (p90) REVERT: c 35 ASP cc_start: 0.7394 (t0) cc_final: 0.6454 (t0) REVERT: d 13 LYS cc_start: 0.8683 (mttt) cc_final: 0.8141 (mtpp) REVERT: d 54 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7478 (ttmm) REVERT: g 73 VAL cc_start: 0.8032 (OUTLIER) cc_final: 0.7629 (m) REVERT: g 99 ASN cc_start: 0.6510 (OUTLIER) cc_final: 0.5611 (m-40) REVERT: g 146 LEU cc_start: 0.7469 (mp) cc_final: 0.6842 (tp) REVERT: g 179 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6209 (mtm) REVERT: g 194 ARG cc_start: 0.8255 (mtt180) cc_final: 0.7345 (mmm160) REVERT: g 210 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.5934 (tp-100) REVERT: g 239 MET cc_start: 0.5454 (OUTLIER) cc_final: 0.4911 (mmm) REVERT: g 256 ARG cc_start: 0.7334 (ttt180) cc_final: 0.6609 (mpp80) REVERT: g 257 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6296 (t80) REVERT: g 273 GLU cc_start: 0.4569 (OUTLIER) cc_final: 0.3900 (mp0) outliers start: 308 outliers final: 220 residues processed: 1036 average time/residue: 0.7690 time to fit residues: 1356.1876 Evaluate side-chains 1051 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 786 time to evaluate : 4.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 104 ARG Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain H residue 29 ASN Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 138 LYS Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 69 GLN Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain P residue 123 TYR Chi-restraints excluded: chain P residue 127 ARG Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 120 ASP Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 128 PHE Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 53 TRP Chi-restraints excluded: chain T residue 97 SER Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 127 ASN Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 33 GLN Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain V residue 50 TYR Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 GLN Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 5 SER Chi-restraints excluded: chain W residue 15 ASN Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 70 ASN Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 30 LYS Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 98 GLU Chi-restraints excluded: chain a residue 8 ASN Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain a residue 32 LYS Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 37 LYS Chi-restraints excluded: chain a residue 39 MET Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 64 CYS Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 27 GLN Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 48 VAL Chi-restraints excluded: chain d residue 54 LYS Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 99 LYS Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 67 HIS Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 176 SER Chi-restraints excluded: chain g residue 179 MET Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 203 ASN Chi-restraints excluded: chain g residue 210 GLN Chi-restraints excluded: chain g residue 239 MET Chi-restraints excluded: chain g residue 240 ASN Chi-restraints excluded: chain g residue 245 ASP Chi-restraints excluded: chain g residue 257 PHE Chi-restraints excluded: chain g residue 273 GLU Chi-restraints excluded: chain g residue 297 VAL Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain g residue 315 ASN Chi-restraints excluded: chain g residue 321 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 397 optimal weight: 0.9980 chunk 256 optimal weight: 0.9990 chunk 383 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 408 optimal weight: 0.7980 chunk 437 optimal weight: 2.9990 chunk 317 optimal weight: 20.0000 chunk 59 optimal weight: 0.5980 chunk 505 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 ASN D 195 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN N 5 HIS N 21 ASN O 29 HIS ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 ASN R 101 ASN ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 HIS W 64 GLN a 8 ASN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 27 GLN g 65 HIS g 210 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.7587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 85640 Z= 0.180 Angle : 0.677 18.817 125161 Z= 0.341 Chirality : 0.038 0.289 15716 Planarity : 0.006 0.146 8655 Dihedral : 24.740 179.980 35742 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 1.42 % Allowed : 9.53 % Favored : 89.05 % Rotamer: Outliers : 6.18 % Allowed : 29.08 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.57 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.12), residues: 4776 helix: 1.41 (0.13), residues: 1507 sheet: -1.20 (0.17), residues: 836 loop : -2.90 (0.11), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 48 HIS 0.011 0.001 HIS S 99 PHE 0.053 0.002 PHE D 24 TYR 0.030 0.002 TYR G 156 ARG 0.020 0.001 ARG J 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 824 time to evaluate : 4.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7602 (pp20) cc_final: 0.7317 (pp20) REVERT: A 200 ASP cc_start: 0.8485 (t70) cc_final: 0.7979 (t0) REVERT: A 204 TYR cc_start: 0.8648 (t80) cc_final: 0.8287 (t80) REVERT: B 47 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6787 (pp) REVERT: B 90 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6741 (tm-30) REVERT: B 148 ASN cc_start: 0.7627 (m110) cc_final: 0.7081 (t0) REVERT: B 196 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8234 (tt0) REVERT: B 223 PHE cc_start: 0.7973 (m-80) cc_final: 0.7576 (t80) REVERT: C 227 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.5765 (t80) REVERT: C 245 MET cc_start: 0.7288 (mmm) cc_final: 0.6905 (mtp) REVERT: D 24 PHE cc_start: 0.5573 (m-80) cc_final: 0.4958 (m-80) REVERT: D 61 GLU cc_start: 0.6704 (mp0) cc_final: 0.6334 (mm-30) REVERT: D 64 ARG cc_start: 0.5867 (ttm170) cc_final: 0.5576 (ttt180) REVERT: D 65 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6883 (mtp85) REVERT: D 90 ARG cc_start: 0.7880 (mtt180) cc_final: 0.6801 (ptm160) REVERT: D 92 HIS cc_start: 0.7277 (m90) cc_final: 0.6726 (t70) REVERT: D 116 ARG cc_start: 0.8188 (mtt90) cc_final: 0.7982 (mtm180) REVERT: D 143 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6647 (ttp80) REVERT: D 187 LYS cc_start: 0.8466 (mttt) cc_final: 0.8029 (mtpp) REVERT: D 190 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.7027 (ptpp) REVERT: E 6 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6855 (mttt) REVERT: E 40 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7422 (tm-30) REVERT: E 162 VAL cc_start: 0.9275 (t) cc_final: 0.9042 (m) REVERT: F 42 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7244 (tt) REVERT: F 51 GLU cc_start: 0.7350 (tt0) cc_final: 0.7085 (tp30) REVERT: F 92 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.7935 (t) REVERT: F 192 ILE cc_start: 0.7325 (OUTLIER) cc_final: 0.6997 (mt) REVERT: G 4 ASN cc_start: 0.7986 (t0) cc_final: 0.7769 (t0) REVERT: G 39 GLU cc_start: 0.6974 (mp0) cc_final: 0.6389 (pp20) REVERT: G 64 LYS cc_start: 0.8701 (tptm) cc_final: 0.8442 (tttm) REVERT: G 96 SER cc_start: 0.8851 (t) cc_final: 0.8178 (p) REVERT: G 125 THR cc_start: 0.5468 (OUTLIER) cc_final: 0.5183 (p) REVERT: G 145 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: G 196 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8276 (mttp) REVERT: H 7 LYS cc_start: 0.7225 (mmtt) cc_final: 0.6758 (mptt) REVERT: H 71 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.6091 (m-70) REVERT: H 147 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.7683 (m110) REVERT: H 165 LYS cc_start: 0.8762 (mttt) cc_final: 0.8163 (mtmm) REVERT: I 84 HIS cc_start: 0.8524 (t70) cc_final: 0.7925 (t-90) REVERT: I 103 GLN cc_start: 0.7897 (mt0) cc_final: 0.7475 (mt0) REVERT: I 158 ASP cc_start: 0.7070 (m-30) cc_final: 0.6736 (m-30) REVERT: I 170 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7350 (mp) REVERT: J 37 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7264 (ttmm) REVERT: J 68 LYS cc_start: 0.7622 (mttt) cc_final: 0.7187 (tttp) REVERT: J 102 GLU cc_start: 0.8322 (mp0) cc_final: 0.7947 (mp0) REVERT: J 115 LYS cc_start: 0.8564 (mttt) cc_final: 0.8197 (mmtm) REVERT: J 145 SER cc_start: 0.8062 (m) cc_final: 0.7753 (p) REVERT: K 54 PHE cc_start: 0.5480 (m-10) cc_final: 0.5164 (m-80) REVERT: K 75 TYR cc_start: 0.5902 (OUTLIER) cc_final: 0.4957 (m-80) REVERT: K 76 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6478 (tt) REVERT: K 77 ARG cc_start: 0.7037 (mtt90) cc_final: 0.6553 (mtt90) REVERT: K 84 GLU cc_start: 0.5667 (mm-30) cc_final: 0.5427 (mm-30) REVERT: L 32 LYS cc_start: 0.7908 (tppt) cc_final: 0.7242 (ttpt) REVERT: L 46 LYS cc_start: 0.7156 (mttt) cc_final: 0.6309 (ptpt) REVERT: L 140 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8850 (mp) REVERT: N 62 GLN cc_start: 0.8625 (mp10) cc_final: 0.8303 (mp10) REVERT: O 53 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7768 (t0) REVERT: O 124 ASP cc_start: 0.6231 (t0) cc_final: 0.5905 (t0) REVERT: P 24 LYS cc_start: 0.6746 (mmpt) cc_final: 0.6148 (mmpt) REVERT: P 28 MET cc_start: 0.7430 (mmm) cc_final: 0.6365 (ptm) REVERT: P 108 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7562 (tpt-90) REVERT: Q 21 HIS cc_start: 0.7431 (m-70) cc_final: 0.6650 (m-70) REVERT: R 18 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6909 (mm-30) REVERT: R 62 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7558 (tm-30) REVERT: R 105 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7837 (mm-40) REVERT: R 106 THR cc_start: 0.8725 (m) cc_final: 0.8491 (p) REVERT: S 11 PHE cc_start: 0.4982 (OUTLIER) cc_final: 0.4765 (m-10) REVERT: S 21 ASN cc_start: 0.8070 (t0) cc_final: 0.7864 (t0) REVERT: T 115 GLU cc_start: 0.8085 (tt0) cc_final: 0.7389 (mm-30) REVERT: U 27 THR cc_start: 0.7449 (OUTLIER) cc_final: 0.6886 (p) REVERT: U 32 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8082 (mtmm) REVERT: V 2 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7835 (mm-30) REVERT: W 15 ASN cc_start: 0.8650 (t0) cc_final: 0.7909 (t0) REVERT: W 20 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8589 (m) REVERT: W 54 ASP cc_start: 0.8625 (t70) cc_final: 0.8305 (t0) REVERT: X 30 LYS cc_start: 0.8828 (ttmp) cc_final: 0.8392 (tttt) REVERT: X 137 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8120 (mmmm) REVERT: Y 18 LEU cc_start: 0.8254 (mt) cc_final: 0.8046 (mt) REVERT: Y 26 ASP cc_start: 0.7965 (t0) cc_final: 0.7728 (t0) REVERT: Y 39 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7877 (tt0) REVERT: Y 68 LYS cc_start: 0.8161 (tttt) cc_final: 0.7945 (tttp) REVERT: Y 83 LYS cc_start: 0.8297 (tttp) cc_final: 0.8037 (mmtt) REVERT: Y 99 LYS cc_start: 0.6767 (tptt) cc_final: 0.6514 (tttp) REVERT: Z 78 VAL cc_start: 0.7812 (t) cc_final: 0.7436 (p) REVERT: Z 92 VAL cc_start: 0.8144 (t) cc_final: 0.7743 (t) REVERT: a 32 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7949 (ttpp) REVERT: a 33 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: a 46 GLU cc_start: 0.7523 (pm20) cc_final: 0.7213 (pm20) REVERT: b 36 LYS cc_start: 0.7470 (tttt) cc_final: 0.7147 (tttp) REVERT: b 63 LEU cc_start: 0.6902 (mp) cc_final: 0.6692 (mp) REVERT: c 31 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6757 (mt-10) REVERT: c 32 PHE cc_start: 0.5875 (OUTLIER) cc_final: 0.4227 (p90) REVERT: c 35 ASP cc_start: 0.7569 (t0) cc_final: 0.6739 (t0) REVERT: c 38 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7570 (ttp80) REVERT: d 13 LYS cc_start: 0.8678 (mttt) cc_final: 0.8151 (mtpp) REVERT: f 89 LYS cc_start: 0.1790 (OUTLIER) cc_final: 0.1524 (tptp) REVERT: g 73 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.7904 (m) REVERT: g 99 ASN cc_start: 0.6325 (OUTLIER) cc_final: 0.5502 (m-40) REVERT: g 146 LEU cc_start: 0.7382 (mp) cc_final: 0.6821 (tp) REVERT: g 179 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6083 (mtm) REVERT: g 210 GLN cc_start: 0.6555 (OUTLIER) cc_final: 0.5918 (tp-100) REVERT: g 256 ARG cc_start: 0.7202 (ttt180) cc_final: 0.6716 (mpp80) REVERT: g 257 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6411 (t80) REVERT: g 273 GLU cc_start: 0.4843 (OUTLIER) cc_final: 0.4269 (mp0) outliers start: 254 outliers final: 168 residues processed: 985 average time/residue: 0.7748 time to fit residues: 1298.1475 Evaluate side-chains 971 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 770 time to evaluate : 4.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 104 ARG Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain H residue 29 ASN Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 69 GLN Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain P residue 123 TYR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 87 ASN Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 53 TRP Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 33 GLN Chi-restraints excluded: chain V residue 74 GLN Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 70 ASN Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain a residue 8 ASN Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain a residue 32 LYS Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 37 LYS Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 64 CYS Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 48 VAL Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 89 LYS Chi-restraints excluded: chain f residue 99 LYS Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain f residue 142 CYS Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 100 SER Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 176 SER Chi-restraints excluded: chain g residue 179 MET Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 210 GLN Chi-restraints excluded: chain g residue 240 ASN Chi-restraints excluded: chain g residue 245 ASP Chi-restraints excluded: chain g residue 257 PHE Chi-restraints excluded: chain g residue 273 GLU Chi-restraints excluded: chain g residue 297 VAL Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain g residue 315 ASN Chi-restraints excluded: chain g residue 321 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 584 optimal weight: 10.0000 chunk 615 optimal weight: 10.0000 chunk 561 optimal weight: 10.0000 chunk 599 optimal weight: 10.0000 chunk 360 optimal weight: 6.9990 chunk 260 optimal weight: 0.7980 chunk 470 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 541 optimal weight: 40.0000 chunk 566 optimal weight: 9.9990 chunk 596 optimal weight: 10.0000 overall best weight: 7.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN D 179 GLN D 195 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 HIS K 47 GLN K 85 HIS N 21 ASN P 103 ASN Q 83 GLN R 101 ASN ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 HIS ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 95 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.7940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 85640 Z= 0.475 Angle : 0.910 19.032 125161 Z= 0.452 Chirality : 0.047 0.318 15716 Planarity : 0.008 0.173 8655 Dihedral : 24.894 179.947 35728 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 1.40 % Allowed : 12.86 % Favored : 85.74 % Rotamer: Outliers : 6.96 % Allowed : 28.25 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.09 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.12), residues: 4776 helix: 0.69 (0.13), residues: 1515 sheet: -1.43 (0.17), residues: 849 loop : -3.05 (0.11), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP B 29 HIS 0.011 0.002 HIS A 23 PHE 0.045 0.003 PHE P 119 TYR 0.027 0.003 TYR A 175 ARG 0.018 0.001 ARG J 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 801 time to evaluate : 4.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7648 (pp20) cc_final: 0.7386 (pp20) REVERT: A 200 ASP cc_start: 0.8456 (t70) cc_final: 0.8106 (t0) REVERT: A 204 TYR cc_start: 0.8540 (t80) cc_final: 0.8258 (t80) REVERT: B 47 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7341 (pt) REVERT: B 62 LYS cc_start: 0.7890 (mmtm) cc_final: 0.7665 (mmtm) REVERT: B 90 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6792 (tm-30) REVERT: B 199 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.7372 (m110) REVERT: B 223 PHE cc_start: 0.7798 (m-80) cc_final: 0.7199 (t80) REVERT: C 227 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.5514 (t80) REVERT: C 245 MET cc_start: 0.7123 (mmm) cc_final: 0.6755 (mtt) REVERT: D 61 GLU cc_start: 0.7033 (mp0) cc_final: 0.6539 (mm-30) REVERT: D 64 ARG cc_start: 0.6303 (ttm170) cc_final: 0.5692 (ttt180) REVERT: D 65 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6882 (mtp180) REVERT: D 90 ARG cc_start: 0.7897 (mtt180) cc_final: 0.6876 (ptm160) REVERT: D 91 VAL cc_start: 0.6300 (OUTLIER) cc_final: 0.5983 (m) REVERT: D 92 HIS cc_start: 0.7333 (m90) cc_final: 0.6806 (t70) REVERT: D 143 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6740 (ttp80) REVERT: D 187 LYS cc_start: 0.8696 (mttt) cc_final: 0.8198 (mtpp) REVERT: D 190 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7312 (ptpp) REVERT: E 6 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7146 (mtpt) REVERT: E 162 VAL cc_start: 0.9338 (t) cc_final: 0.9084 (m) REVERT: F 51 GLU cc_start: 0.7276 (tt0) cc_final: 0.7064 (tp30) REVERT: F 92 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8336 (t) REVERT: G 4 ASN cc_start: 0.8331 (t0) cc_final: 0.7972 (t0) REVERT: G 17 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7195 (tp30) REVERT: G 64 LYS cc_start: 0.8687 (tptm) cc_final: 0.8327 (tttm) REVERT: G 96 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8544 (p) REVERT: G 125 THR cc_start: 0.5711 (OUTLIER) cc_final: 0.5383 (p) REVERT: G 145 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: G 156 TYR cc_start: 0.5302 (m-80) cc_final: 0.4816 (m-80) REVERT: G 196 LYS cc_start: 0.8587 (mmtt) cc_final: 0.8186 (mttp) REVERT: H 7 LYS cc_start: 0.7380 (mmtt) cc_final: 0.6932 (mptt) REVERT: H 70 TYR cc_start: 0.6820 (m-10) cc_final: 0.6571 (m-10) REVERT: H 71 HIS cc_start: 0.7215 (OUTLIER) cc_final: 0.6042 (m-70) REVERT: H 88 ARG cc_start: 0.7900 (mpt-90) cc_final: 0.7566 (mmt90) REVERT: H 147 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.7812 (m110) REVERT: H 169 PHE cc_start: 0.7839 (m-10) cc_final: 0.7630 (m-10) REVERT: I 161 PHE cc_start: 0.7644 (m-80) cc_final: 0.7379 (m-80) REVERT: I 170 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7198 (mp) REVERT: J 37 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7872 (ttmm) REVERT: J 68 LYS cc_start: 0.7547 (mttt) cc_final: 0.7227 (tttp) REVERT: J 115 LYS cc_start: 0.8819 (mttt) cc_final: 0.8445 (mmtp) REVERT: K 75 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.4957 (m-80) REVERT: K 76 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6463 (tt) REVERT: K 77 ARG cc_start: 0.7019 (mtt90) cc_final: 0.6590 (mtt90) REVERT: L 32 LYS cc_start: 0.8212 (tppt) cc_final: 0.7621 (ttpt) REVERT: L 43 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8068 (mmtp) REVERT: L 46 LYS cc_start: 0.7257 (mttt) cc_final: 0.6082 (ptpt) REVERT: L 50 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7109 (mp0) REVERT: L 131 ILE cc_start: 0.8087 (mp) cc_final: 0.7815 (mp) REVERT: L 140 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8715 (mp) REVERT: N 18 TYR cc_start: 0.6613 (OUTLIER) cc_final: 0.5339 (p90) REVERT: N 62 GLN cc_start: 0.8764 (mp10) cc_final: 0.8438 (mp10) REVERT: O 124 ASP cc_start: 0.6932 (t0) cc_final: 0.6559 (t0) REVERT: P 24 LYS cc_start: 0.6748 (mmpt) cc_final: 0.6173 (mmpt) REVERT: P 28 MET cc_start: 0.7456 (mmm) cc_final: 0.6342 (ptm) REVERT: P 108 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7584 (tpt-90) REVERT: Q 21 HIS cc_start: 0.7840 (m-70) cc_final: 0.6804 (m-70) REVERT: R 105 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7665 (mp10) REVERT: S 11 PHE cc_start: 0.5126 (OUTLIER) cc_final: 0.4875 (m-10) REVERT: S 21 ASN cc_start: 0.8063 (t0) cc_final: 0.7837 (t0) REVERT: S 85 PHE cc_start: 0.7152 (t80) cc_final: 0.6731 (t80) REVERT: T 38 LYS cc_start: 0.7772 (tttt) cc_final: 0.7523 (tttm) REVERT: T 48 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.6863 (mt0) REVERT: T 115 GLU cc_start: 0.8187 (tt0) cc_final: 0.7453 (mm-30) REVERT: U 27 THR cc_start: 0.7605 (OUTLIER) cc_final: 0.7049 (p) REVERT: U 32 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8091 (mtmm) REVERT: V 2 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8007 (mm-30) REVERT: W 15 ASN cc_start: 0.8745 (t0) cc_final: 0.8002 (t0) REVERT: W 20 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8644 (m) REVERT: W 54 ASP cc_start: 0.8810 (t70) cc_final: 0.8493 (t0) REVERT: X 30 LYS cc_start: 0.8905 (ttmp) cc_final: 0.8555 (tttt) REVERT: X 137 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8364 (mmmm) REVERT: Y 68 LYS cc_start: 0.8385 (tttt) cc_final: 0.8006 (tttp) REVERT: Y 99 LYS cc_start: 0.7332 (tptt) cc_final: 0.6861 (tttp) REVERT: Z 78 VAL cc_start: 0.7859 (t) cc_final: 0.7504 (p) REVERT: a 32 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8133 (ttpp) REVERT: b 36 LYS cc_start: 0.7531 (tttt) cc_final: 0.7159 (tttp) REVERT: c 31 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7207 (mt-10) REVERT: c 32 PHE cc_start: 0.6045 (OUTLIER) cc_final: 0.4578 (p90) REVERT: d 13 LYS cc_start: 0.8706 (mttt) cc_final: 0.8102 (mtpp) REVERT: d 54 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7849 (ttmm) REVERT: f 89 LYS cc_start: 0.1535 (OUTLIER) cc_final: 0.1277 (tptp) REVERT: g 11 ARG cc_start: 0.7320 (ttp-110) cc_final: 0.7119 (ttp-110) REVERT: g 73 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.7912 (m) REVERT: g 99 ASN cc_start: 0.6795 (OUTLIER) cc_final: 0.5780 (m-40) REVERT: g 135 TRP cc_start: 0.7831 (m100) cc_final: 0.7609 (m100) REVERT: g 146 LEU cc_start: 0.7517 (mp) cc_final: 0.6849 (tp) REVERT: g 179 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6265 (mtm) REVERT: g 194 ARG cc_start: 0.8259 (mtt180) cc_final: 0.7387 (mmm160) REVERT: g 210 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.6911 (tp-100) REVERT: g 239 MET cc_start: 0.5864 (OUTLIER) cc_final: 0.5655 (mmp) REVERT: g 256 ARG cc_start: 0.7268 (ttt180) cc_final: 0.6653 (mpp-170) REVERT: g 257 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.5951 (t80) REVERT: g 273 GLU cc_start: 0.4002 (OUTLIER) cc_final: 0.2941 (mp0) outliers start: 286 outliers final: 212 residues processed: 997 average time/residue: 0.7984 time to fit residues: 1361.9525 Evaluate side-chains 1008 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 760 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain H residue 29 ASN Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 28 ASN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 69 GLN Chi-restraints excluded: chain N residue 18 TYR Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 123 TYR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 53 TRP Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 127 ASN Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 30 SER Chi-restraints excluded: chain V residue 33 GLN Chi-restraints excluded: chain V residue 74 GLN Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 5 SER Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 70 ASN Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 13 ILE Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain a residue 32 LYS Chi-restraints excluded: chain a residue 37 LYS Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 94 ILE Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 64 CYS Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 46 LYS Chi-restraints excluded: chain d residue 54 LYS Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 89 LYS Chi-restraints excluded: chain f residue 99 LYS Chi-restraints excluded: chain f residue 106 TYR Chi-restraints excluded: chain f residue 113 LYS Chi-restraints excluded: chain f residue 142 CYS Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 100 SER Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 176 SER Chi-restraints excluded: chain g residue 179 MET Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 199 PHE Chi-restraints excluded: chain g residue 203 ASN Chi-restraints excluded: chain g residue 210 GLN Chi-restraints excluded: chain g residue 239 MET Chi-restraints excluded: chain g residue 240 ASN Chi-restraints excluded: chain g residue 245 ASP Chi-restraints excluded: chain g residue 257 PHE Chi-restraints excluded: chain g residue 273 GLU Chi-restraints excluded: chain g residue 297 VAL Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain g residue 315 ASN Chi-restraints excluded: chain g residue 321 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 393 optimal weight: 6.9990 chunk 633 optimal weight: 20.0000 chunk 386 optimal weight: 8.9990 chunk 300 optimal weight: 0.9990 chunk 440 optimal weight: 7.9990 chunk 664 optimal weight: 30.0000 chunk 611 optimal weight: 9.9990 chunk 529 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 408 optimal weight: 5.9990 chunk 324 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 124 ASN E 130 GLN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 HIS I 53 GLN ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 GLN ** b 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 210 GLN g 231 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.8032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 85640 Z= 0.266 Angle : 0.754 18.005 125161 Z= 0.379 Chirality : 0.041 0.284 15716 Planarity : 0.006 0.147 8655 Dihedral : 24.831 179.925 35724 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 1.38 % Allowed : 10.36 % Favored : 88.25 % Rotamer: Outliers : 5.40 % Allowed : 30.24 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.09 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.12), residues: 4776 helix: 0.97 (0.13), residues: 1514 sheet: -1.29 (0.18), residues: 832 loop : -2.96 (0.11), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP g 46 HIS 0.008 0.001 HIS S 99 PHE 0.062 0.002 PHE D 24 TYR 0.030 0.002 TYR G 156 ARG 0.017 0.001 ARG J 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9552 Ramachandran restraints generated. 4776 Oldfield, 0 Emsley, 4776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 794 time to evaluate : 6.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7676 (pp20) cc_final: 0.7447 (pp20) REVERT: A 200 ASP cc_start: 0.8552 (t70) cc_final: 0.8122 (t0) REVERT: A 204 TYR cc_start: 0.8558 (t80) cc_final: 0.8291 (t80) REVERT: B 47 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7175 (pp) REVERT: B 199 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.7464 (m110) REVERT: B 223 PHE cc_start: 0.7739 (m-80) cc_final: 0.7157 (t80) REVERT: C 227 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.5842 (t80) REVERT: C 245 MET cc_start: 0.6922 (mmm) cc_final: 0.6541 (mtt) REVERT: D 61 GLU cc_start: 0.6851 (mp0) cc_final: 0.6444 (mm-30) REVERT: D 64 ARG cc_start: 0.6170 (ttm170) cc_final: 0.5782 (ttt180) REVERT: D 65 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6906 (mtp180) REVERT: D 90 ARG cc_start: 0.7950 (mtt180) cc_final: 0.6857 (ptm160) REVERT: D 92 HIS cc_start: 0.7312 (m90) cc_final: 0.6770 (t70) REVERT: D 143 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6636 (ttp80) REVERT: D 187 LYS cc_start: 0.8664 (mttt) cc_final: 0.8323 (mtpp) REVERT: D 190 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7100 (ptpp) REVERT: E 6 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.7052 (mtpt) REVERT: E 40 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7554 (tm-30) REVERT: E 97 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7361 (mm-30) REVERT: E 162 VAL cc_start: 0.9305 (t) cc_final: 0.9051 (m) REVERT: F 51 GLU cc_start: 0.7342 (tt0) cc_final: 0.7084 (tp30) REVERT: F 92 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8199 (t) REVERT: G 39 GLU cc_start: 0.7401 (mp0) cc_final: 0.7016 (mm-30) REVERT: G 64 LYS cc_start: 0.8707 (tptm) cc_final: 0.8362 (tttm) REVERT: G 113 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8656 (tt) REVERT: G 125 THR cc_start: 0.5710 (OUTLIER) cc_final: 0.5492 (p) REVERT: G 145 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: G 156 TYR cc_start: 0.5405 (m-80) cc_final: 0.4819 (m-80) REVERT: G 196 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8191 (mttp) REVERT: H 7 LYS cc_start: 0.7364 (mmtt) cc_final: 0.6904 (mptt) REVERT: H 88 ARG cc_start: 0.7887 (mpt-90) cc_final: 0.7545 (mmt90) REVERT: H 147 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.7731 (m110) REVERT: H 165 LYS cc_start: 0.8810 (mttt) cc_final: 0.8296 (mtmm) REVERT: I 84 HIS cc_start: 0.8647 (t70) cc_final: 0.8060 (t-90) REVERT: I 103 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8476 (mm-40) REVERT: I 170 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7129 (mp) REVERT: J 37 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7575 (ttmm) REVERT: J 65 LYS cc_start: 0.7880 (tptp) cc_final: 0.7580 (tppt) REVERT: J 68 LYS cc_start: 0.7452 (mttt) cc_final: 0.7144 (tttm) REVERT: J 110 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7157 (mt0) REVERT: J 115 LYS cc_start: 0.8716 (mttt) cc_final: 0.8368 (mmtp) REVERT: J 145 SER cc_start: 0.8411 (m) cc_final: 0.7814 (p) REVERT: K 75 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.4921 (m-80) REVERT: K 76 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6404 (tt) REVERT: K 77 ARG cc_start: 0.6966 (mtt90) cc_final: 0.6478 (mtt90) REVERT: K 84 GLU cc_start: 0.5180 (mm-30) cc_final: 0.4833 (mm-30) REVERT: L 32 LYS cc_start: 0.8177 (tppt) cc_final: 0.7665 (ttpt) REVERT: L 43 LYS cc_start: 0.8413 (mmtt) cc_final: 0.7961 (mmtp) REVERT: L 46 LYS cc_start: 0.7089 (mttt) cc_final: 0.6317 (ptpt) REVERT: L 131 ILE cc_start: 0.8147 (mp) cc_final: 0.7940 (mt) REVERT: L 140 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8753 (mp) REVERT: N 18 TYR cc_start: 0.6503 (OUTLIER) cc_final: 0.5237 (p90) REVERT: N 62 GLN cc_start: 0.8682 (mp10) cc_final: 0.8355 (mp10) REVERT: O 124 ASP cc_start: 0.6478 (t0) cc_final: 0.6216 (t0) REVERT: P 24 LYS cc_start: 0.6882 (mmpt) cc_final: 0.6215 (mmpt) REVERT: P 28 MET cc_start: 0.7505 (mmm) cc_final: 0.6542 (ptm) REVERT: P 105 VAL cc_start: 0.7801 (p) cc_final: 0.7437 (m) REVERT: P 108 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7587 (tpt-90) REVERT: Q 21 HIS cc_start: 0.7656 (m-70) cc_final: 0.6642 (m-70) REVERT: R 18 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7232 (mm-30) REVERT: R 71 PHE cc_start: 0.2784 (m-10) cc_final: 0.2186 (m-10) REVERT: R 105 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7464 (mp10) REVERT: R 106 THR cc_start: 0.8682 (m) cc_final: 0.8447 (p) REVERT: S 11 PHE cc_start: 0.5134 (OUTLIER) cc_final: 0.4880 (m-10) REVERT: T 48 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.6682 (mt0) REVERT: T 115 GLU cc_start: 0.8136 (tt0) cc_final: 0.7400 (mm-30) REVERT: U 27 THR cc_start: 0.7743 (OUTLIER) cc_final: 0.7220 (p) REVERT: U 32 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8072 (mtmm) REVERT: V 2 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7947 (mm-30) REVERT: V 10 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: W 15 ASN cc_start: 0.8625 (t0) cc_final: 0.7894 (t0) REVERT: W 20 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8620 (m) REVERT: W 54 ASP cc_start: 0.8702 (t70) cc_final: 0.8310 (t0) REVERT: X 30 LYS cc_start: 0.8837 (ttmp) cc_final: 0.8500 (tttt) REVERT: X 137 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8209 (mmmm) REVERT: Y 39 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8153 (tt0) REVERT: Y 68 LYS cc_start: 0.8314 (tttt) cc_final: 0.7973 (tttp) REVERT: Y 83 LYS cc_start: 0.8357 (tttp) cc_final: 0.8049 (mmtt) REVERT: Y 99 LYS cc_start: 0.7078 (tptt) cc_final: 0.6776 (tttp) REVERT: Z 78 VAL cc_start: 0.8183 (t) cc_final: 0.7800 (p) REVERT: a 32 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8098 (ttpp) REVERT: b 36 LYS cc_start: 0.7491 (tttt) cc_final: 0.7093 (tttp) REVERT: c 31 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7031 (mt-10) REVERT: c 32 PHE cc_start: 0.5901 (OUTLIER) cc_final: 0.4306 (p90) REVERT: d 13 LYS cc_start: 0.8771 (mttt) cc_final: 0.8162 (mtpp) REVERT: d 54 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7573 (ttmm) REVERT: f 89 LYS cc_start: 0.1413 (OUTLIER) cc_final: 0.1171 (tptp) REVERT: g 11 ARG cc_start: 0.7272 (ttp-110) cc_final: 0.7020 (ttp-110) REVERT: g 73 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.7923 (m) REVERT: g 99 ASN cc_start: 0.6617 (OUTLIER) cc_final: 0.5600 (m-40) REVERT: g 146 LEU cc_start: 0.7412 (mp) cc_final: 0.6752 (tp) REVERT: g 179 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6261 (mtm) REVERT: g 194 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7349 (mmm160) REVERT: g 210 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7317 (tp40) REVERT: g 256 ARG cc_start: 0.7260 (ttt180) cc_final: 0.6635 (mpp-170) REVERT: g 257 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6610 (t80) REVERT: g 273 GLU cc_start: 0.4008 (OUTLIER) cc_final: 0.2855 (mp0) outliers start: 222 outliers final: 172 residues processed: 949 average time/residue: 0.7584 time to fit residues: 1230.2364 Evaluate side-chains 979 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 772 time to evaluate : 4.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 104 ARG Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain H residue 29 ASN Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 63 TYR Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 69 GLN Chi-restraints excluded: chain N residue 18 TYR Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain P residue 123 TYR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 53 TRP Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 127 ASN Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain V residue 10 GLU Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 30 SER Chi-restraints excluded: chain V residue 33 GLN Chi-restraints excluded: chain V residue 71 ARG Chi-restraints excluded: chain V residue 74 GLN Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 5 SER Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 70 ASN Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 96 LEU Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain a residue 32 LYS Chi-restraints excluded: chain a residue 37 LYS Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 94 ILE Chi-restraints excluded: chain b residue 27 SER Chi-restraints excluded: chain b residue 64 CYS Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 54 LYS Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 89 LYS Chi-restraints excluded: chain f residue 99 LYS Chi-restraints excluded: chain f residue 113 LYS Chi-restraints excluded: chain f residue 142 CYS Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 99 ASN Chi-restraints excluded: chain g residue 100 SER Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 176 SER Chi-restraints excluded: chain g residue 179 MET Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 203 ASN Chi-restraints excluded: chain g residue 210 GLN Chi-restraints excluded: chain g residue 240 ASN Chi-restraints excluded: chain g residue 257 PHE Chi-restraints excluded: chain g residue 273 GLU Chi-restraints excluded: chain g residue 297 VAL Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain g residue 315 ASN Chi-restraints excluded: chain g residue 321 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 420 optimal weight: 0.9980 chunk 563 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 487 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 529 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 544 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 ASN B 209 ASN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 43 ASN ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.177534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.139985 restraints weight = 122413.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139445 restraints weight = 150181.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141376 restraints weight = 111944.700| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.8156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 85640 Z= 0.241 Angle : 0.728 17.354 125161 Z= 0.365 Chirality : 0.039 0.282 15716 Planarity : 0.006 0.146 8655 Dihedral : 24.736 179.765 35724 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 1.28 % Allowed : 11.45 % Favored : 87.27 % Rotamer: Outliers : 5.55 % Allowed : 30.29 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.09 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.12), residues: 4776 helix: 1.08 (0.13), residues: 1526 sheet: -1.21 (0.18), residues: 818 loop : -2.91 (0.11), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP g 135 HIS 0.008 0.001 HIS g 295 PHE 0.047 0.002 PHE D 24 TYR 0.030 0.002 TYR G 156 ARG 0.021 0.001 ARG G 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20585.91 seconds wall clock time: 362 minutes 34.14 seconds (21754.14 seconds total)