Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 14:19:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5it9_8124/04_2023/5it9_8124.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5it9_8124/04_2023/5it9_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_8124/04_2023/5it9_8124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5it9_8124/04_2023/5it9_8124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5it9_8124/04_2023/5it9_8124.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5it9_8124/04_2023/5it9_8124.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 111 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: 83 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: 31.03, per 1000 atoms: 0.39 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: 32.24 Conformation dependent library (CDL) restraints added in 4.5 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: 21.96 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: 61.09 Time building geometry restraints manager: 34.85 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: 43981 35.97 - 71.94: 3200 71.94 - 107.91: 268 107.91 - 143.88: 35 143.88 - 179.85: 81 Dihedral angle restraints: 47565 sinusoidal: 33589 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 47562 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: 1.510 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: 10.750 Check model and map are aligned: 0.930 Set scattering table: 0.560 Process input model: 216.470 Find NCS groups from input model: 1.920 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: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 234.890 ------------------------------------------------------------------------------- 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 : 21.507 179.853 38547 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 % 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 *********************** 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 : 4.524 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 388 outliers final: 73 residues processed: 1654 average time/residue: 0.8888 time to fit residues: 2363.0876 Evaluate side-chains 883 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 810 time to evaluate : 4.717 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 1 residues processed: 73 average time/residue: 0.6350 time to fit residues: 92.2742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 563 optimal weight: 10.0000 chunk 505 optimal weight: 10.0000 chunk 280 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 341 optimal weight: 1.9990 chunk 270 optimal weight: 6.9990 chunk 522 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 chunk 317 optimal weight: 5.9990 chunk 389 optimal weight: 10.0000 chunk 605 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 101 HIS B 118 GLN B 211 HIS C 64 HIS C 115 HIS D 92 HIS ** D 101 GLN ** 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 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 GLN G 210 GLN H 71 HIS H 160 GLN H 170 GLN ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 HIS I 53 GLN I 116 HIS ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 HIS M 76 ASN N 21 ASN N 49 GLN N 58 HIS N 101 HIS N 123 HIS N 151 ASN ** 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 55 HIS ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN T 85 ASN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 HIS ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 ASN W 117 HIS X 18 HIS Y 22 GLN Y 29 HIS ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 82 HIS a 8 ASN d 20 GLN 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: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.127 85640 Z= 0.398 Angle : 0.965 17.422 125161 Z= 0.486 Chirality : 0.052 0.406 15716 Planarity : 0.008 0.160 8655 Dihedral : 20.155 179.960 28962 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 1.80 % Allowed : 9.65 % Favored : 88.55 % Rotamer Outliers : 5.99 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.09 % 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: -1.97 (0.12), residues: 4776 helix: 1.87 (0.13), residues: 1523 sheet: -2.06 (0.16), residues: 817 loop : -3.33 (0.10), residues: 2436 *********************** 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 1198 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 952 time to evaluate : 4.659 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 outliers start: 246 outliers final: 113 residues processed: 1113 average time/residue: 0.7909 time to fit residues: 1492.0631 Evaluate side-chains 882 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 769 time to evaluate : 4.512 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 0 residues processed: 113 average time/residue: 0.6168 time to fit residues: 136.9681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 336 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 504 optimal weight: 10.0000 chunk 412 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 606 optimal weight: 9.9990 chunk 655 optimal weight: 40.0000 chunk 540 optimal weight: 40.0000 chunk 601 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 486 optimal weight: 10.0000 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 69 ASN B 124 ASN B 208 GLN D 159 HIS ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS E 223 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN F 188 ASN G 4 ASN ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 HIS I 53 GLN ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN L 37 ASN ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 HIS ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 HIS Q 94 GLN S 75 ASN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 ASN U 98 HIS V 81 ASN W 15 ASN X 75 GLN X 79 ASN Y 29 HIS b 5 GLN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 123 ASN g 79 ASN g 292 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.164 85640 Z= 0.305 Angle : 0.807 15.273 125161 Z= 0.413 Chirality : 0.045 0.322 15716 Planarity : 0.007 0.154 8655 Dihedral : 19.674 179.733 28962 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 1.68 % Allowed : 10.95 % Favored : 87.37 % Rotamer Outliers : 5.52 % 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: -1.82 (0.12), residues: 4776 helix: 1.76 (0.13), residues: 1501 sheet: -1.87 (0.16), residues: 826 loop : -3.07 (0.11), residues: 2449 *********************** 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 1096 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 869 time to evaluate : 4.628 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 outliers start: 227 outliers final: 103 residues processed: 1014 average time/residue: 0.7840 time to fit residues: 1352.2461 Evaluate side-chains 853 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 750 time to evaluate : 4.576 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 0 residues processed: 103 average time/residue: 0.6238 time to fit residues: 125.3552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 314 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 289 optimal weight: 10.0000 chunk 407 optimal weight: 6.9990 chunk 608 optimal weight: 10.0000 chunk 644 optimal weight: 10.0000 chunk 318 optimal weight: 7.9990 chunk 577 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 92 GLN B 209 ASN F 65 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN G 182 GLN H 174 ASN H 180 GLN I 20 GLN I 53 GLN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 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** R 101 ASN S 75 ASN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN T 101 ASN U 98 HIS V 74 GLN W 117 HIS a 8 ASN c 27 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.106 85640 Z= 0.334 Angle : 0.815 16.706 125161 Z= 0.410 Chirality : 0.044 0.364 15716 Planarity : 0.007 0.149 8655 Dihedral : 19.494 179.552 28962 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 1.61 % Allowed : 9.90 % Favored : 88.48 % Rotamer Outliers : 4.31 % 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: -1.96 (0.12), residues: 4776 helix: 1.28 (0.13), residues: 1524 sheet: -1.64 (0.17), residues: 803 loop : -3.05 (0.11), residues: 2449 *********************** 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 1031 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 854 time to evaluate : 5.859 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 outliers start: 177 outliers final: 105 residues processed: 950 average time/residue: 0.8019 time to fit residues: 1315.4274 Evaluate side-chains 856 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 751 time to evaluate : 4.592 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 0 residues processed: 105 average time/residue: 0.6514 time to fit residues: 132.6010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0060 chunk 9 optimal weight: 7.9990 chunk 480 optimal weight: 10.0000 chunk 266 optimal weight: 3.9990 chunk 550 optimal weight: 30.0000 chunk 445 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 329 optimal weight: 9.9990 chunk 578 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 overall best weight: 5.2004 ------------------------------------------------------------------------------- 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 49 ASN B 124 ASN C 99 GLN E 8 HIS ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN F 118 HIS G 139 ASN H 42 GLN H 180 GLN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN K 47 GLN K 85 HIS L 110 HIS ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN O 12 GLN R 101 ASN S 75 ASN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN T 101 ASN U 98 HIS W 44 HIS X 79 ASN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 27 GLN g 51 ASN g 231 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.6657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.091 85640 Z= 0.371 Angle : 0.841 20.065 125161 Z= 0.423 Chirality : 0.045 0.304 15716 Planarity : 0.007 0.150 8655 Dihedral : 19.463 179.900 28962 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 1.72 % Allowed : 10.85 % Favored : 87.44 % Rotamer Outliers : 4.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 2.62 % 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: -2.07 (0.12), residues: 4776 helix: 1.01 (0.13), residues: 1519 sheet: -1.51 (0.18), residues: 822 loop : -3.05 (0.11), residues: 2435 *********************** 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 999 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 821 time to evaluate : 4.690 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 outliers start: 178 outliers final: 88 residues processed: 941 average time/residue: 0.7904 time to fit residues: 1272.3323 Evaluate side-chains 831 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 743 time to evaluate : 4.685 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 0 residues processed: 88 average time/residue: 0.6527 time to fit residues: 112.1135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 378 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 645 optimal weight: 10.0000 chunk 535 optimal weight: 40.0000 chunk 298 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 213 optimal weight: 7.9990 chunk 338 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 124 ASN E 96 ASN E 98 ASN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 ASN ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 ASN U 44 ASN U 98 HIS ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 27 GLN g 231 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.7045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 85640 Z= 0.298 Angle : 0.772 15.979 125161 Z= 0.389 Chirality : 0.042 0.292 15716 Planarity : 0.006 0.149 8655 Dihedral : 19.301 179.961 28962 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 1.65 % Allowed : 9.90 % Favored : 88.44 % Rotamer Outliers : 2.82 % 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: -1.92 (0.12), residues: 4776 helix: 1.15 (0.13), residues: 1519 sheet: -1.42 (0.18), residues: 826 loop : -2.97 (0.11), residues: 2431 *********************** 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 911 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 795 time to evaluate : 4.724 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 outliers start: 116 outliers final: 60 residues processed: 862 average time/residue: 0.8076 time to fit residues: 1205.7822 Evaluate side-chains 785 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 725 time to evaluate : 4.595 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.6381 time to fit residues: 76.8695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 367 optimal weight: 4.9990 chunk 471 optimal weight: 8.9990 chunk 365 optimal weight: 0.0970 chunk 543 optimal weight: 10.0000 chunk 360 optimal weight: 2.9990 chunk 642 optimal weight: 20.0000 chunk 402 optimal weight: 2.9990 chunk 391 optimal weight: 5.9990 chunk 296 optimal weight: 0.6980 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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 124 ASN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN M 130 HIS ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 HIS Y 77 ASN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 27 GLN f 132 ASN ** g 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.7244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 85640 Z= 0.219 Angle : 0.714 17.190 125161 Z= 0.361 Chirality : 0.039 0.294 15716 Planarity : 0.006 0.146 8655 Dihedral : 19.120 179.949 28962 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 1.53 % Allowed : 10.01 % Favored : 88.46 % Rotamer Outliers : 2.26 % 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: -1.74 (0.12), residues: 4776 helix: 1.35 (0.14), residues: 1514 sheet: -1.39 (0.17), residues: 840 loop : -2.87 (0.11), residues: 2422 *********************** 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 891 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 798 time to evaluate : 4.599 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 outliers start: 93 outliers final: 48 residues processed: 852 average time/residue: 0.8029 time to fit residues: 1179.7537 Evaluate side-chains 776 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 728 time to evaluate : 4.568 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.6101 time to fit residues: 61.2929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 397 optimal weight: 7.9990 chunk 256 optimal weight: 7.9990 chunk 383 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 chunk 408 optimal weight: 2.9990 chunk 437 optimal weight: 7.9990 chunk 317 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 505 optimal weight: 10.0000 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 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 148 ASN B 177 GLN D 195 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 GLN H 22 GLN H 174 ASN H 180 GLN ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 72 ASN U 98 HIS Y 29 HIS ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 27 GLN ** g 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.7509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 85640 Z= 0.266 Angle : 0.740 15.354 125161 Z= 0.373 Chirality : 0.040 0.283 15716 Planarity : 0.006 0.146 8655 Dihedral : 19.060 179.902 28962 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 1.51 % Allowed : 10.43 % Favored : 88.07 % Rotamer Outliers : 1.73 % 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: -1.77 (0.12), residues: 4776 helix: 1.25 (0.13), residues: 1521 sheet: -1.36 (0.17), residues: 833 loop : -2.86 (0.11), residues: 2422 *********************** 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 837 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 766 time to evaluate : 4.580 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 outliers start: 71 outliers final: 41 residues processed: 798 average time/residue: 0.7956 time to fit residues: 1109.1674 Evaluate side-chains 766 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 725 time to evaluate : 4.501 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.6533 time to fit residues: 56.1844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 260 optimal weight: 5.9990 chunk 470 optimal weight: 10.0000 chunk 183 optimal weight: 30.0000 chunk 541 optimal weight: 40.0000 chunk 566 optimal weight: 10.0000 chunk 596 optimal weight: 10.0000 overall best weight: 7.5996 ------------------------------------------------------------------------------- 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 177 GLN C 157 HIS ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN H 11 GLN H 22 GLN I 103 GLN ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 HIS W 64 GLN Y 29 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.8012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.111 85640 Z= 0.492 Angle : 0.944 16.393 125161 Z= 0.471 Chirality : 0.048 0.309 15716 Planarity : 0.008 0.151 8655 Dihedral : 19.452 179.692 28962 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 1.61 % Allowed : 12.90 % Favored : 85.49 % Rotamer Outliers : 1.85 % 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: -2.33 (0.12), residues: 4776 helix: 0.52 (0.13), residues: 1518 sheet: -1.58 (0.18), residues: 835 loop : -3.04 (0.11), residues: 2423 *********************** 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 838 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 762 time to evaluate : 4.717 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 outliers start: 76 outliers final: 47 residues processed: 801 average time/residue: 0.8011 time to fit residues: 1094.8537 Evaluate side-chains 751 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 704 time to evaluate : 5.997 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.6042 time to fit residues: 59.8114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 393 optimal weight: 10.0000 chunk 633 optimal weight: 20.0000 chunk 386 optimal weight: 4.9990 chunk 300 optimal weight: 0.9980 chunk 440 optimal weight: 0.9990 chunk 664 optimal weight: 30.0000 chunk 611 optimal weight: 9.9990 chunk 529 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 408 optimal weight: 7.9990 chunk 324 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 HIS ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 HIS Y 77 ASN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.8124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 85640 Z= 0.261 Angle : 0.765 23.265 125161 Z= 0.385 Chirality : 0.041 0.276 15716 Planarity : 0.006 0.147 8655 Dihedral : 19.157 179.972 28962 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 1.53 % Allowed : 9.90 % Favored : 88.57 % Rotamer Outliers : 0.68 % 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: -2.01 (0.12), residues: 4776 helix: 0.95 (0.13), residues: 1516 sheet: -1.52 (0.17), residues: 852 loop : -2.92 (0.12), residues: 2408 ********************** 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 801 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 773 time to evaluate : 4.766 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 outliers start: 28 outliers final: 13 residues processed: 784 average time/residue: 0.8053 time to fit residues: 1085.8330 Evaluate side-chains 743 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 730 time to evaluate : 4.578 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.6609 time to fit residues: 21.1549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 420 optimal weight: 10.0000 chunk 563 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 487 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 529 optimal weight: 10.0000 chunk 221 optimal weight: 0.9980 chunk 544 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN B 148 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 HIS ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 HIS ** Y 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.170718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130664 restraints weight = 120776.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.130071 restraints weight = 106753.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132825 restraints weight = 87440.183| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.8275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 85640 Z= 0.311 Angle : 0.789 15.467 125161 Z= 0.396 Chirality : 0.042 0.309 15716 Planarity : 0.006 0.147 8655 Dihedral : 19.111 179.960 28962 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 1.53 % Allowed : 11.91 % Favored : 86.56 % Rotamer Outliers : 0.97 % 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: -2.03 (0.12), residues: 4776 helix: 0.94 (0.13), residues: 1516 sheet: -1.48 (0.18), residues: 822 loop : -2.95 (0.11), residues: 2438 =============================================================================== Job complete usr+sys time: 18951.76 seconds wall clock time: 335 minutes 5.36 seconds (20105.36 seconds total)