Starting phenix.real_space_refine on Tue Feb 20 02:05:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sys_25539/02_2024/7sys_25539.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sys_25539/02_2024/7sys_25539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sys_25539/02_2024/7sys_25539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sys_25539/02_2024/7sys_25539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sys_25539/02_2024/7sys_25539.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sys_25539/02_2024/7sys_25539.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1958 5.49 5 S 187 5.16 5 C 44673 2.51 5 N 15273 2.21 5 O 20889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 6": "OD1" <-> "OD2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 271": "OD1" <-> "OD2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 206": "OD1" <-> "OD2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 124": "OD1" <-> "OD2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "I PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 6": "OD1" <-> "OD2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 107": "OE1" <-> "OE2" Residue "L TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 74": "OE1" <-> "OE2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 67": "OD1" <-> "OD2" Residue "P GLU 87": "OE1" <-> "OE2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "R PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 53": "OE1" <-> "OE2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "R TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 101": "OD1" <-> "OD2" Residue "R TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 123": "OD1" <-> "OD2" Residue "R GLU 128": "OE1" <-> "OE2" Residue "S GLU 18": "OE1" <-> "OE2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 104": "OE1" <-> "OE2" Residue "S PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 8": "OD1" <-> "OD2" Residue "U TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 116": "OD1" <-> "OD2" Residue "V GLU 45": "OE1" <-> "OE2" Residue "V PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 7": "OE1" <-> "OE2" Residue "W ASP 28": "OD1" <-> "OD2" Residue "W ASP 76": "OD1" <-> "OD2" Residue "X ASP 9": "OD1" <-> "OD2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "Y ASP 19": "OD1" <-> "OD2" Residue "Z ASP 53": "OD1" <-> "OD2" Residue "Z ASP 80": "OD1" <-> "OD2" Residue "a TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 6": "OD1" <-> "OD2" Residue "c GLU 14": "OE1" <-> "OE2" Residue "d GLU 33": "OE1" <-> "OE2" Residue "d ASP 54": "OD1" <-> "OD2" Residue "e TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 37": "OD1" <-> "OD2" Residue "h ASP 74": "OD1" <-> "OD2" Residue "h ASP 116": "OD1" <-> "OD2" Residue "h PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 50": "OE1" <-> "OE2" Residue "j GLU 99": "OE1" <-> "OE2" Residue "j PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 82981 Number of models: 1 Model: "" Number of chains: 40 Chain: "2" Number of atoms: 36227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36227 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 143, 'rna2p_pyr': 112, 'rna3p_pur': 754, 'rna3p_pyr': 688} Link IDs: {'rna2p': 254, 'rna3p': 1442} Chain breaks: 11 Chain: "A" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 798 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "F" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} bond proxies already assigned to first conformer: 1709 Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1233 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 997 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "j" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1221 Classifications: {'peptide': 182} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 80} Link IDs: {'PTRANS': 4, 'TRANS': 177} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 10, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 155 Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "z" Number of atoms: 4017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 4017 Classifications: {'RNA': 188} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 17, 'rna3p_pur': 80, 'rna3p_pyr': 74} Link IDs: {'rna2p': 34, 'rna3p': 153} Chain breaks: 1 Chain: "i" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1604 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 62} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 70175 SG CYS b 23 93.204 129.096 131.827 1.00 28.50 S ATOM 70196 SG CYS b 26 97.604 129.865 132.503 1.00 32.83 S ATOM 70579 SG CYS b 74 95.244 126.676 133.098 1.00 27.08 S ATOM 70598 SG CYS b 77 95.057 128.305 134.760 1.00 27.97 S Time building chain proxies: 36.63, per 1000 atoms: 0.44 Number of scatterers: 82981 At special positions: 0 Unit cell: (237.5, 209.95, 262.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 187 16.00 P 1958 15.00 O 20889 8.00 N 15273 7.00 C 44673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 141 " - pdb=" SG CYS g 144 " distance=2.03 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.56 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " Number of angles added : 6 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9608 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 63 sheets defined 35.3% alpha, 17.7% beta 524 base pairs and 1050 stacking pairs defined. Time for finding SS restraints: 25.71 Creating SS restraints... Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.817A pdb=" N VAL B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.917A pdb=" N GLU B 35 " --> pdb=" O PHE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 50 through 68 removed outlier: 4.273A pdb=" N ILE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.624A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 137 removed outlier: 3.910A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 187 Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.923A pdb=" N LEU B 201 " --> pdb=" O MET B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 23 through 26 removed outlier: 3.703A pdb=" N SER C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 23 through 26' Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.629A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.563A pdb=" N GLU C 175 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.514A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.743A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 78 through 84 Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.592A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.521A pdb=" N ALA D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 217 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'D' and resid 269 through 277 removed outlier: 3.603A pdb=" N LYS D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 removed outlier: 3.528A pdb=" N PHE E 11 " --> pdb=" O LYS E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 60 removed outlier: 4.091A pdb=" N LEU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.549A pdb=" N ARG E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY E 78 " --> pdb=" O GLN E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 97 through 112 removed outlier: 3.673A pdb=" N GLY E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.517A pdb=" N VAL E 164 " --> pdb=" O GLY E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 44 through 51 Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.714A pdb=" N VAL F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 119 No H-bonds generated for 'chain 'F' and resid 117 through 119' Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 32 through 36 removed outlier: 3.606A pdb=" N GLN G 36 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 66 Processing helix chain 'G' and resid 67 through 77 removed outlier: 4.024A pdb=" N MET G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 105 removed outlier: 3.813A pdb=" N THR G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 119 Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.599A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 203 removed outlier: 3.879A pdb=" N ASN G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 28 removed outlier: 3.612A pdb=" N TYR H 28 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 42 removed outlier: 3.696A pdb=" N GLY H 42 " --> pdb=" O ASP H 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 39 through 42' Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 237 removed outlier: 3.513A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 34 Processing helix chain 'I' and resid 35 through 40 removed outlier: 4.097A pdb=" N ALA I 38 " --> pdb=" O ASP I 35 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU I 40 " --> pdb=" O LYS I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 75 removed outlier: 3.785A pdb=" N ILE I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 87 removed outlier: 3.616A pdb=" N LEU I 79 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL I 80 " --> pdb=" O GLN I 76 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 4.266A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 88 through 93 removed outlier: 4.438A pdb=" N ARG J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 117 Processing helix chain 'J' and resid 132 through 139 removed outlier: 3.886A pdb=" N ILE J 136 " --> pdb=" O GLU J 132 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU J 137 " --> pdb=" O GLU J 133 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 154 Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 192 through 207 removed outlier: 3.932A pdb=" N GLU J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 39 through 62 removed outlier: 4.234A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 88 through 92 removed outlier: 3.854A pdb=" N MET K 92 " --> pdb=" O GLU K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 108 removed outlier: 3.920A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG K 108 " --> pdb=" O ASP K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 removed outlier: 3.762A pdb=" N GLY K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 150 through 155 removed outlier: 3.550A pdb=" N SER K 153 " --> pdb=" O ARG K 150 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN K 154 " --> pdb=" O LEU K 151 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYS K 155 " --> pdb=" O ASP K 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 150 through 155' Processing helix chain 'K' and resid 171 through 186 removed outlier: 3.677A pdb=" N ARG K 175 " --> pdb=" O GLY K 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.514A pdb=" N GLU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 56 removed outlier: 3.929A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 83 Processing helix chain 'M' and resid 47 through 53 removed outlier: 3.831A pdb=" N ILE M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 29 Processing helix chain 'N' and resid 35 through 45 Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 81 through 90 removed outlier: 4.412A pdb=" N LEU N 85 " --> pdb=" O ASP N 81 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY N 90 " --> pdb=" O GLY N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 130 Processing helix chain 'O' and resid 29 through 43 Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 85 through 103 Processing helix chain 'O' and resid 108 through 132 removed outlier: 3.539A pdb=" N TYR O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 149 removed outlier: 3.805A pdb=" N ALA O 148 " --> pdb=" O SER O 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 62 removed outlier: 4.053A pdb=" N VAL P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 58 through 62' Processing helix chain 'P' and resid 70 through 89 Processing helix chain 'P' and resid 111 through 122 Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.250A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 46 Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'Q' and resid 86 through 90 removed outlier: 3.637A pdb=" N VAL Q 90 " --> pdb=" O PRO Q 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 42 No H-bonds generated for 'chain 'R' and resid 40 through 42' Processing helix chain 'R' and resid 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' Processing helix chain 'R' and resid 47 through 59 Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 77 through 100 removed outlier: 3.843A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.820A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 27 through 38 Processing helix chain 'S' and resid 44 through 64 removed outlier: 3.801A pdb=" N ARG S 63 " --> pdb=" O LYS S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 83 Processing helix chain 'S' and resid 99 through 110 removed outlier: 3.836A pdb=" N ASP S 110 " --> pdb=" O LEU S 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 18 removed outlier: 3.591A pdb=" N ASN T 17 " --> pdb=" O ARG T 14 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR T 18 " --> pdb=" O VAL T 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 14 through 18' Processing helix chain 'T' and resid 25 through 30 removed outlier: 4.160A pdb=" N ILE T 30 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.767A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.675A pdb=" N LYS T 78 " --> pdb=" O ARG T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 84 removed outlier: 3.890A pdb=" N LEU T 84 " --> pdb=" O ASP T 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 118 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'T' and resid 140 through 144 removed outlier: 3.936A pdb=" N GLY T 143 " --> pdb=" O GLY T 140 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG T 144 " --> pdb=" O ARG T 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 140 through 144' Processing helix chain 'U' and resid 10 through 26 removed outlier: 3.664A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 67 removed outlier: 4.058A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 removed outlier: 3.563A pdb=" N TYR U 79 " --> pdb=" O MET U 75 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 110 removed outlier: 3.721A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 143 Processing helix chain 'V' and resid 29 through 46 Processing helix chain 'V' and resid 94 through 103 removed outlier: 3.635A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 Processing helix chain 'W' and resid 65 through 77 Processing helix chain 'X' and resid 5 through 21 Processing helix chain 'X' and resid 31 through 44 Processing helix chain 'X' and resid 85 through 94 removed outlier: 3.745A pdb=" N TRP X 89 " --> pdb=" O ASP X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 119 Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 25 through 30 Processing helix chain 'Y' and resid 33 through 38 Processing helix chain 'Y' and resid 89 through 94 removed outlier: 3.743A pdb=" N ASN Y 92 " --> pdb=" O GLY Y 89 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE Y 93 " --> pdb=" O CYS Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 36 through 49 removed outlier: 3.799A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 Processing helix chain 'Z' and resid 87 through 95 removed outlier: 3.857A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 117 removed outlier: 3.904A pdb=" N VAL Z 117 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 removed outlier: 3.953A pdb=" N ASN Z 124 " --> pdb=" O THR Z 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 62 removed outlier: 3.737A pdb=" N TYR a 55 " --> pdb=" O ASP a 51 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP a 56 " --> pdb=" O LYS a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 65 No H-bonds generated for 'chain 'a' and resid 63 through 65' Processing helix chain 'a' and resid 69 through 78 Processing helix chain 'a' and resid 80 through 94 Processing helix chain 'b' and resid 49 through 56 removed outlier: 3.504A pdb=" N ALA b 56 " --> pdb=" O ASP b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'c' and resid 11 through 18 Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 32 through 36 removed outlier: 3.678A pdb=" N GLY e 35 " --> pdb=" O ARG e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 46 Processing helix chain 'e' and resid 46 through 51 removed outlier: 3.793A pdb=" N ILE e 50 " --> pdb=" O TYR e 46 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY e 51 " --> pdb=" O ALA e 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 46 through 51' Processing helix chain 'f' and resid 83 through 89 Processing helix chain 'f' and resid 103 through 116 removed outlier: 3.712A pdb=" N ARG f 107 " --> pdb=" O GLY f 103 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 105 Processing helix chain 'j' and resid 38 through 40 No H-bonds generated for 'chain 'j' and resid 38 through 40' Processing helix chain 'j' and resid 58 through 62 removed outlier: 3.919A pdb=" N LEU j 62 " --> pdb=" O ILE j 59 " (cutoff:3.500A) Processing helix chain 'j' and resid 94 through 120 Processing helix chain 'j' and resid 123 through 135 Processing helix chain 'j' and resid 135 through 143 Processing helix chain 'j' and resid 146 through 157 removed outlier: 4.384A pdb=" N TYR j 150 " --> pdb=" O GLY j 146 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP j 151 " --> pdb=" O TYR j 147 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA j 152 " --> pdb=" O GLY j 148 " (cutoff:3.500A) Processing helix chain 'j' and resid 159 through 164 removed outlier: 3.825A pdb=" N LEU j 163 " --> pdb=" O ASP j 159 " (cutoff:3.500A) Processing helix chain 'j' and resid 170 through 184 Processing helix chain 'n' and resid 2 through 24 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 removed outlier: 3.702A pdb=" N ARG A 57 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 49 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU A 48 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE A 76 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS A 94 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 78 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP A 90 " --> pdb=" O GLY A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 41 removed outlier: 7.071A pdb=" N ILE B 48 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.637A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER B 75 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL B 124 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 50 removed outlier: 4.529A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 43 through 50 removed outlier: 4.529A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ARG C 213 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL C 210 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE C 142 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL C 212 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 140 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 136 " --> pdb=" O LYS C 216 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 137 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 125 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS C 139 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA C 123 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 103 through 116 removed outlier: 6.027A pdb=" N ASP D 104 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N GLY D 131 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY D 119 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D 128 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 140 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.667A pdb=" N SER D 225 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR D 224 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 36 through 42 removed outlier: 3.923A pdb=" N GLY E 36 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU E 47 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU E 85 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE E 48 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 148 through 155 removed outlier: 3.562A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP E 154 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS E 134 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 209 through 210 removed outlier: 3.908A pdb=" N SER E 209 " --> pdb=" O ILE S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 224 through 226 removed outlier: 3.752A pdb=" N GLU E 225 " --> pdb=" O ASN h 187 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN h 187 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL h 176 " --> pdb=" O LYS h 185 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASN h 187 " --> pdb=" O VAL h 174 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL h 174 " --> pdb=" O ASN h 187 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 9 through 10 removed outlier: 4.397A pdb=" N LEU F 9 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB5, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.573A pdb=" N GLU F 97 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN F 98 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.604A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA F 110 " --> pdb=" O ILE F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.621A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR F 159 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE F 172 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN F 161 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 217 through 221 removed outlier: 3.615A pdb=" N THR F 220 " --> pdb=" O VAL F 208 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 229 through 230 removed outlier: 3.512A pdb=" N LYS F 230 " --> pdb=" O LYS F 233 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS F 233 " --> pdb=" O LYS F 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 123 through 127 removed outlier: 18.516A pdb=" N ARG G 136 " --> pdb=" O ILE d 43 " (cutoff:3.500A) removed outlier: 13.447A pdb=" N ASN d 45 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ALA G 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N LYS d 47 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 12 through 17 removed outlier: 6.888A pdb=" N LYS H 2 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU H 111 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASN H 4 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE H 113 " --> pdb=" O ASN H 4 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER H 6 " --> pdb=" O ILE H 113 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N LYS H 115 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL H 108 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY H 55 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASN H 110 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL H 114 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.536A pdb=" N VAL H 97 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 75 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 48 through 52 removed outlier: 3.784A pdb=" N ILE I 51 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA I 59 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 185 through 188 removed outlier: 3.702A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 37 through 38 removed outlier: 6.202A pdb=" N LYS J 37 " --> pdb=" O LEU J 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'J' and resid 45 through 47 Processing sheet with id=AC8, first strand: chain 'J' and resid 62 through 67 removed outlier: 3.675A pdb=" N PHE J 65 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG J 74 " --> pdb=" O PHE J 65 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE J 78 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP J 105 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE J 101 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA J 185 " --> pdb=" O VAL J 62 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 135 through 137 removed outlier: 3.510A pdb=" N ASP K 158 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 20 through 24 removed outlier: 3.833A pdb=" N MET L 21 " --> pdb=" O TRP L 69 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA L 23 " --> pdb=" O PHE L 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 72 through 79 removed outlier: 6.999A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N SER M 110 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL M 142 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY M 129 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS M 144 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 91 through 96 removed outlier: 3.640A pdb=" N TYR M 92 " --> pdb=" O ARG M 105 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE M 96 " --> pdb=" O ARG M 101 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG M 101 " --> pdb=" O ILE M 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 31 through 32 removed outlier: 3.806A pdb=" N VAL N 111 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU N 49 " --> pdb=" O VAL N 111 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 52 through 53 removed outlier: 6.914A pdb=" N LEU N 52 " --> pdb=" O VAL N 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'P' and resid 52 through 57 removed outlier: 7.070A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR P 57 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR P 40 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY P 29 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LYS P 96 " --> pdb=" O GLY P 29 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS P 31 " --> pdb=" O LYS P 96 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ARG P 98 " --> pdb=" O CYS P 31 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE P 33 " --> pdb=" O ARG P 98 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU P 93 " --> pdb=" O ILE P 126 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ARG P 128 " --> pdb=" O LEU P 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 76 through 77 removed outlier: 6.983A pdb=" N VAL Q 76 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N TYR Q 97 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 9 through 10 removed outlier: 3.626A pdb=" N LYS R 26 " --> pdb=" O ASP R 67 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 9 through 10 removed outlier: 3.626A pdb=" N LYS R 26 " --> pdb=" O ASP R 67 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU R 31 " --> pdb=" O VAL R 66 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 96 through 98 removed outlier: 6.085A pdb=" N ILE S 96 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'T' and resid 12 through 13 Processing sheet with id=AE3, first strand: chain 'U' and resid 81 through 83 Processing sheet with id=AE4, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AE5, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.545A pdb=" N LEU V 88 " --> pdb=" O VAL V 54 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.545A pdb=" N LEU V 88 " --> pdb=" O VAL V 54 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 63 through 66 Processing sheet with id=AE8, first strand: chain 'W' and resid 32 through 39 removed outlier: 4.915A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 24 through 27 Processing sheet with id=AF1, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.765A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE X 130 " --> pdb=" O LYS X 71 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL X 103 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE X 128 " --> pdb=" O PHE X 101 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE X 101 " --> pdb=" O PHE X 128 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 128 through 129 removed outlier: 6.659A pdb=" N LEU Y 101 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL Y 125 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N GLU Y 99 " --> pdb=" O VAL Y 125 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL Y 51 " --> pdb=" O GLN Y 73 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN Y 73 " --> pdb=" O VAL Y 51 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU Y 53 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE Y 120 " --> pdb=" O THR Y 82 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 6 through 15 removed outlier: 4.498A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LYS Z 68 " --> pdb=" O THR Z 62 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR Z 62 " --> pdb=" O LYS Z 68 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 67 through 68 removed outlier: 7.063A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AF6, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.704A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'c' and resid 44 through 47 removed outlier: 3.532A pdb=" N MET c 33 " --> pdb=" O VAL c 46 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'c' and resid 64 through 65 Processing sheet with id=AF9, first strand: chain 'e' and resid 30 through 31 removed outlier: 3.952A pdb=" N MET e 38 " --> pdb=" O ILE e 31 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 106 through 108 Processing sheet with id=AG2, first strand: chain 'g' and resid 138 through 139 Processing sheet with id=AG3, first strand: chain 'h' and resid 5 through 12 removed outlier: 6.976A pdb=" N VAL h 309 " --> pdb=" O ARG h 8 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR h 10 " --> pdb=" O VAL h 307 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL h 307 " --> pdb=" O THR h 10 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU h 306 " --> pdb=" O TYR h 302 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER h 288 " --> pdb=" O GLY h 301 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 18 through 22 removed outlier: 5.903A pdb=" N ILE h 40 " --> pdb=" O ALA h 58 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA h 58 " --> pdb=" O ILE h 40 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N MET h 42 " --> pdb=" O GLN h 56 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'h' and resid 66 through 71 removed outlier: 6.283A pdb=" N LEU h 87 " --> pdb=" O ARG h 100 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG h 100 " --> pdb=" O LEU h 87 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU h 89 " --> pdb=" O THR h 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'h' and resid 108 through 113 Processing sheet with id=AG7, first strand: chain 'h' and resid 195 through 200 removed outlier: 4.814A pdb=" N GLY h 211 " --> pdb=" O GLN h 215 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLN h 215 " --> pdb=" O GLY h 211 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU h 230 " --> pdb=" O ALA h 216 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'h' and resid 236 through 241 removed outlier: 6.487A pdb=" N ALA h 251 " --> pdb=" O ASN h 237 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU h 239 " --> pdb=" O CYS h 249 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N CYS h 249 " --> pdb=" O LEU h 239 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N PHE h 241 " --> pdb=" O TRP h 247 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TRP h 247 " --> pdb=" O PHE h 241 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU h 248 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE h 258 " --> pdb=" O ASP h 268 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP h 268 " --> pdb=" O ILE h 258 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASP h 260 " --> pdb=" O ILE h 266 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE h 266 " --> pdb=" O ASP h 260 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'j' and resid 43 through 44 removed outlier: 3.614A pdb=" N VAL j 34 " --> pdb=" O GLY j 44 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER j 35 " --> pdb=" O VAL j 24 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL j 24 " --> pdb=" O SER j 35 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP j 84 " --> pdb=" O ILE j 74 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL j 76 " --> pdb=" O TYR j 82 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR j 82 " --> pdb=" O VAL j 76 " (cutoff:3.500A) 1540 hydrogen bonds defined for protein. 4431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1320 hydrogen bonds 2220 hydrogen bond angles 0 basepair planarities 524 basepair parallelities 1050 stacking parallelities Total time for adding SS restraints: 66.42 Time building geometry restraints manager: 33.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12393 1.33 - 1.45: 33566 1.45 - 1.58: 38466 1.58 - 1.70: 3904 1.70 - 1.82: 285 Bond restraints: 88614 Sorted by residual: bond pdb=" CD2 TRP j 136 " pdb=" CE2 TRP j 136 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.70e-02 3.46e+03 1.74e+01 bond pdb=" CD2 TRP j 136 " pdb=" CE3 TRP j 136 " ideal model delta sigma weight residual 1.398 1.456 -0.058 1.60e-02 3.91e+03 1.30e+01 bond pdb=" CA ASN Z 85 " pdb=" CB ASN Z 85 " ideal model delta sigma weight residual 1.526 1.571 -0.045 1.51e-02 4.39e+03 8.69e+00 bond pdb=" CD GLU j 99 " pdb=" OE1 GLU j 99 " ideal model delta sigma weight residual 1.249 1.208 0.041 1.90e-02 2.77e+03 4.71e+00 bond pdb=" C THR E 42 " pdb=" N PRO E 43 " ideal model delta sigma weight residual 1.332 1.353 -0.021 1.12e-02 7.97e+03 3.66e+00 ... (remaining 88609 not shown) Histogram of bond angle deviations from ideal: 98.59 - 106.21: 11709 106.21 - 113.82: 53415 113.82 - 121.44: 41377 121.44 - 129.06: 21042 129.06 - 136.67: 1495 Bond angle restraints: 129038 Sorted by residual: angle pdb=" CD2 TRP j 136 " pdb=" CE3 TRP j 136 " pdb=" CZ3 TRP j 136 " ideal model delta sigma weight residual 118.60 129.63 -11.03 1.30e+00 5.92e-01 7.19e+01 angle pdb=" CA GLU j 99 " pdb=" CB GLU j 99 " pdb=" CG GLU j 99 " ideal model delta sigma weight residual 114.10 126.39 -12.29 2.00e+00 2.50e-01 3.78e+01 angle pdb=" C VAL G 141 " pdb=" N SER G 142 " pdb=" CA SER G 142 " ideal model delta sigma weight residual 120.68 129.81 -9.13 1.52e+00 4.33e-01 3.61e+01 angle pdb=" CE2 TRP j 136 " pdb=" CD2 TRP j 136 " pdb=" CE3 TRP j 136 " ideal model delta sigma weight residual 118.80 124.72 -5.92 1.00e+00 1.00e+00 3.51e+01 angle pdb=" CA GLU L 13 " pdb=" CB GLU L 13 " pdb=" CG GLU L 13 " ideal model delta sigma weight residual 114.10 125.52 -11.42 2.00e+00 2.50e-01 3.26e+01 ... (remaining 129033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 51248 35.91 - 71.82: 4648 71.82 - 107.73: 610 107.73 - 143.64: 10 143.64 - 179.55: 31 Dihedral angle restraints: 56547 sinusoidal: 41659 harmonic: 14888 Sorted by residual: dihedral pdb=" O4' C 21303 " pdb=" C1' C 21303 " pdb=" N1 C 21303 " pdb=" C2 C 21303 " ideal model delta sinusoidal sigma weight residual 200.00 34.17 165.83 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 2.17 -162.17 1 1.50e+01 4.44e-03 8.33e+01 dihedral pdb=" O4' C 21206 " pdb=" C1' C 21206 " pdb=" N1 C 21206 " pdb=" C2 C 21206 " ideal model delta sinusoidal sigma weight residual -160.00 -0.53 -159.47 1 1.50e+01 4.44e-03 8.26e+01 ... (remaining 56544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 14359 0.063 - 0.126: 1454 0.126 - 0.190: 161 0.190 - 0.253: 36 0.253 - 0.316: 10 Chirality restraints: 16020 Sorted by residual: chirality pdb=" C3' G 2 874 " pdb=" C4' G 2 874 " pdb=" O3' G 2 874 " pdb=" C2' G 2 874 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" C3' U 2 553 " pdb=" C4' U 2 553 " pdb=" O3' U 2 553 " pdb=" C2' U 2 553 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ASP B 44 " pdb=" N ASP B 44 " pdb=" C ASP B 44 " pdb=" CB ASP B 44 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 16017 not shown) Planarity restraints: 9106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN Y 61 " -0.078 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO Y 62 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO Y 62 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO Y 62 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS N 72 " 0.019 2.00e-02 2.50e+03 2.49e-02 9.27e+00 pdb=" CG HIS N 72 " -0.053 2.00e-02 2.50e+03 pdb=" ND1 HIS N 72 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS N 72 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS N 72 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS N 72 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO Q 68 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.63e+00 pdb=" N PRO Q 69 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO Q 69 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO Q 69 " 0.041 5.00e-02 4.00e+02 ... (remaining 9103 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 17208 2.79 - 3.32: 65950 3.32 - 3.84: 157467 3.84 - 4.37: 183362 4.37 - 4.90: 269842 Nonbonded interactions: 693829 Sorted by model distance: nonbonded pdb=" OP1 U z 127 " pdb=" O2' G z 313 " model vdw 2.259 2.440 nonbonded pdb=" OP2 C 2 98 " pdb=" O2' A 2 426 " model vdw 2.263 2.440 nonbonded pdb=" OP1 G 21654 " pdb=" OG SER U 90 " model vdw 2.284 2.440 nonbonded pdb=" OG SER h 72 " pdb=" OD1 ASP h 74 " model vdw 2.292 2.440 nonbonded pdb=" O2 C 21705 " pdb=" O2' A 21851 " model vdw 2.294 2.440 ... (remaining 693824 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=0.50 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: 3.260 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: 0.060 Extract box with map and model: 16.880 Check model and map are aligned: 0.920 Set scattering table: 0.710 Process input model: 237.530 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 263.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 0.003 0.071 88614 Z= 0.190 Angle : 0.747 14.018 129038 Z= 0.373 Chirality : 0.040 0.316 16020 Planarity : 0.006 0.116 9106 Dihedral : 21.899 179.549 46936 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.11 % Allowed : 0.36 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.42 (0.10), residues: 5104 helix: -1.39 (0.10), residues: 1603 sheet: -0.82 (0.18), residues: 849 loop : -2.01 (0.10), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 117 HIS 0.031 0.001 HIS N 72 PHE 0.035 0.002 PHE N 128 TYR 0.038 0.002 TYR C 205 ARG 0.018 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 936 time to evaluate : 4.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LYS cc_start: 0.7675 (tttp) cc_final: 0.7456 (tttm) REVERT: D 72 ASP cc_start: 0.7981 (m-30) cc_final: 0.7764 (m-30) REVERT: D 221 ASP cc_start: 0.7601 (m-30) cc_final: 0.7346 (m-30) REVERT: E 170 THR cc_start: 0.7496 (m) cc_final: 0.7157 (m) REVERT: G 104 THR cc_start: 0.8370 (p) cc_final: 0.8150 (p) REVERT: H 121 ILE cc_start: 0.7100 (mm) cc_final: 0.6447 (tt) REVERT: H 225 GLN cc_start: 0.6577 (mt0) cc_final: 0.6035 (tp-100) REVERT: I 72 PHE cc_start: 0.7736 (m-80) cc_final: 0.7380 (m-80) REVERT: I 132 ASP cc_start: 0.6717 (m-30) cc_final: 0.5344 (m-30) REVERT: P 114 SER cc_start: 0.8102 (t) cc_final: 0.7792 (m) REVERT: S 126 MET cc_start: 0.7444 (ttm) cc_final: 0.7241 (ttm) REVERT: T 65 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7127 (mp0) REVERT: T 73 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7489 (t0) REVERT: T 89 ASP cc_start: 0.6141 (t70) cc_final: 0.5776 (t70) REVERT: X 31 SER cc_start: 0.8274 (t) cc_final: 0.8035 (t) REVERT: Z 13 MET cc_start: 0.7722 (tmm) cc_final: 0.7346 (tmm) REVERT: d 54 ASP cc_start: 0.7493 (p0) cc_final: 0.6846 (p0) REVERT: g 94 LYS cc_start: 0.5960 (ptpp) cc_final: 0.5541 (mmtp) REVERT: h 181 ASN cc_start: 0.5641 (p0) cc_final: 0.4563 (t0) REVERT: h 217 MET cc_start: 0.6957 (mtp) cc_final: 0.6156 (mtp) REVERT: j 67 ARG cc_start: 0.7328 (ttp-170) cc_final: 0.7081 (ttp-170) REVERT: n 14 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7971 (mmmt) outliers start: 4 outliers final: 3 residues processed: 938 average time/residue: 0.8390 time to fit residues: 1304.1641 Evaluate side-chains 654 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 650 time to evaluate : 4.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 73 ASN Chi-restraints excluded: chain j residue 142 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 150 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 587 optimal weight: 5.9990 chunk 527 optimal weight: 5.9990 chunk 292 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 355 optimal weight: 0.0980 chunk 281 optimal weight: 4.9990 chunk 545 optimal weight: 7.9990 chunk 211 optimal weight: 0.9990 chunk 331 optimal weight: 5.9990 chunk 406 optimal weight: 5.9990 chunk 632 optimal weight: 0.7980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN E 74 GLN F 138 HIS H 197 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN N 72 HIS S 118 GLN ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 117 GLN c 51 GLN c 84 HIS ** h 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 40 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 88614 Z= 0.186 Angle : 0.539 10.874 129038 Z= 0.275 Chirality : 0.035 0.226 16020 Planarity : 0.005 0.075 9106 Dihedral : 22.828 179.390 36416 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.39 % Allowed : 8.86 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.28 (0.11), residues: 5104 helix: 0.32 (0.13), residues: 1656 sheet: -0.62 (0.17), residues: 902 loop : -1.75 (0.11), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP j 136 HIS 0.009 0.001 HIS N 72 PHE 0.024 0.001 PHE I 19 TYR 0.028 0.001 TYR g 105 ARG 0.007 0.000 ARG g 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 687 time to evaluate : 4.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 GLU cc_start: 0.6426 (pt0) cc_final: 0.5754 (pt0) REVERT: D 72 ASP cc_start: 0.8009 (m-30) cc_final: 0.7730 (m-30) REVERT: F 87 MET cc_start: 0.7340 (mtp) cc_final: 0.7117 (mtt) REVERT: F 182 MET cc_start: 0.7497 (ttt) cc_final: 0.7162 (ttt) REVERT: F 237 SER cc_start: 0.8232 (p) cc_final: 0.8022 (p) REVERT: G 78 MET cc_start: 0.6744 (mtt) cc_final: 0.6481 (mtt) REVERT: H 121 ILE cc_start: 0.6967 (mm) cc_final: 0.6401 (tt) REVERT: H 225 GLN cc_start: 0.6597 (mt0) cc_final: 0.6046 (tp-100) REVERT: I 131 GLU cc_start: 0.6860 (pp20) cc_final: 0.6425 (pp20) REVERT: I 132 ASP cc_start: 0.6619 (m-30) cc_final: 0.6367 (m-30) REVERT: L 14 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8086 (tp) REVERT: P 132 VAL cc_start: 0.8575 (m) cc_final: 0.8254 (p) REVERT: Q 106 GLU cc_start: 0.7373 (tp30) cc_final: 0.7052 (tp30) REVERT: T 89 ASP cc_start: 0.6553 (t70) cc_final: 0.6239 (t70) REVERT: Z 13 MET cc_start: 0.7683 (tmm) cc_final: 0.7252 (tmm) REVERT: d 54 ASP cc_start: 0.7539 (p0) cc_final: 0.6861 (p0) REVERT: g 94 LYS cc_start: 0.6032 (ptpp) cc_final: 0.5577 (mmtp) outliers start: 60 outliers final: 44 residues processed: 719 average time/residue: 0.7905 time to fit residues: 968.8686 Evaluate side-chains 675 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 630 time to evaluate : 6.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 127 LYS Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain V residue 18 HIS Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain X residue 30 CYS Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 129 SER Chi-restraints excluded: chain Z residue 78 SER Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain g residue 107 LYS Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 142 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 150 TYR Chi-restraints excluded: chain n residue 13 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 351 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 526 optimal weight: 8.9990 chunk 430 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 633 optimal weight: 20.0000 chunk 684 optimal weight: 20.0000 chunk 563 optimal weight: 9.9990 chunk 627 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 507 optimal weight: 20.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN C 179 ASN D 235 ASN G 83 ASN H 110 ASN K 132 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 HIS O 5 HIS Q 54 HIS Q 79 HIS S 83 ASN ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 91 ASN X 113 HIS ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 88614 Z= 0.206 Angle : 0.550 9.622 129038 Z= 0.281 Chirality : 0.036 0.246 16020 Planarity : 0.004 0.075 9106 Dihedral : 22.769 179.226 36414 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.19 % Allowed : 12.87 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.81 (0.12), residues: 5104 helix: 0.94 (0.13), residues: 1665 sheet: -0.54 (0.17), residues: 903 loop : -1.58 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 7 HIS 0.008 0.001 HIS P 43 PHE 0.029 0.002 PHE Y 105 TYR 0.019 0.002 TYR g 105 ARG 0.007 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 695 time to evaluate : 4.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 GLN cc_start: 0.8283 (tp-100) cc_final: 0.8047 (mm-40) REVERT: C 89 GLU cc_start: 0.6320 (pt0) cc_final: 0.5745 (pt0) REVERT: D 72 ASP cc_start: 0.8004 (m-30) cc_final: 0.7728 (m-30) REVERT: F 19 MET cc_start: 0.8330 (mtm) cc_final: 0.8095 (mtm) REVERT: F 182 MET cc_start: 0.7462 (ttt) cc_final: 0.7222 (ttt) REVERT: F 237 SER cc_start: 0.8405 (p) cc_final: 0.8175 (p) REVERT: F 251 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6942 (mt-10) REVERT: H 121 ILE cc_start: 0.6959 (mm) cc_final: 0.6357 (tt) REVERT: H 192 ILE cc_start: 0.8793 (mm) cc_final: 0.8372 (mt) REVERT: H 225 GLN cc_start: 0.6561 (mt0) cc_final: 0.6027 (tp-100) REVERT: L 72 THR cc_start: 0.7159 (OUTLIER) cc_final: 0.6894 (p) REVERT: M 7 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7097 (mt-10) REVERT: M 109 MET cc_start: 0.8126 (ptt) cc_final: 0.7899 (ptp) REVERT: N 112 LYS cc_start: 0.5123 (mptt) cc_final: 0.4318 (mmtp) REVERT: P 96 LYS cc_start: 0.8384 (mttt) cc_final: 0.7930 (mmtt) REVERT: P 131 ASP cc_start: 0.7754 (t0) cc_final: 0.7383 (t0) REVERT: P 132 VAL cc_start: 0.8580 (m) cc_final: 0.8307 (p) REVERT: Q 82 ASP cc_start: 0.8362 (p0) cc_final: 0.7993 (p0) REVERT: Q 106 GLU cc_start: 0.7259 (tp30) cc_final: 0.7035 (tp30) REVERT: S 77 GLU cc_start: 0.7250 (mp0) cc_final: 0.6716 (mp0) REVERT: T 61 GLU cc_start: 0.7609 (mp0) cc_final: 0.7396 (mp0) REVERT: T 89 ASP cc_start: 0.6735 (t70) cc_final: 0.6396 (t70) REVERT: W 64 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7217 (mt-10) REVERT: W 78 ILE cc_start: 0.8531 (mm) cc_final: 0.8221 (mt) REVERT: X 91 ASN cc_start: 0.8176 (m-40) cc_final: 0.7856 (m110) REVERT: Z 13 MET cc_start: 0.7763 (tmm) cc_final: 0.7403 (tmm) REVERT: Z 74 MET cc_start: 0.7712 (mpp) cc_final: 0.7150 (mpp) REVERT: g 94 LYS cc_start: 0.6125 (ptpp) cc_final: 0.5600 (mmtp) REVERT: h 140 TYR cc_start: 0.6132 (t80) cc_final: 0.5919 (t80) REVERT: n 14 LYS cc_start: 0.8328 (mmmt) cc_final: 0.7910 (mtmt) REVERT: n 21 ARG cc_start: 0.6516 (tpt170) cc_final: 0.6262 (mtp-110) outliers start: 95 outliers final: 65 residues processed: 749 average time/residue: 0.7737 time to fit residues: 990.9767 Evaluate side-chains 705 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 639 time to evaluate : 4.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 235 SER Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 132 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain O residue 31 ASP Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 89 MET Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain V residue 18 HIS Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain X residue 30 CYS Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 129 SER Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 55 ILE Chi-restraints excluded: chain Z residue 78 SER Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain g residue 107 LYS Chi-restraints excluded: chain h residue 181 ASN Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 142 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 150 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 625 optimal weight: 8.9990 chunk 476 optimal weight: 10.0000 chunk 328 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 302 optimal weight: 10.0000 chunk 425 optimal weight: 0.0060 chunk 635 optimal weight: 0.0370 chunk 672 optimal weight: 40.0000 chunk 331 optimal weight: 10.0000 chunk 602 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 overall best weight: 4.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN C 147 ASN F 17 HIS G 83 ASN ** I 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN S 62 GLN S 83 ASN ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 GLN j 41 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 88614 Z= 0.272 Angle : 0.586 10.846 129038 Z= 0.300 Chirality : 0.038 0.273 16020 Planarity : 0.005 0.057 9106 Dihedral : 22.816 179.863 36414 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.94 % Allowed : 15.08 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.80 (0.12), residues: 5104 helix: 1.02 (0.13), residues: 1663 sheet: -0.64 (0.17), residues: 899 loop : -1.58 (0.12), residues: 2542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 7 HIS 0.007 0.001 HIS T 135 PHE 0.026 0.002 PHE Y 105 TYR 0.017 0.002 TYR L 78 ARG 0.014 0.001 ARG K 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 659 time to evaluate : 4.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.3864 (mptt) cc_final: 0.2102 (ttmm) REVERT: B 52 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8119 (mttt) REVERT: D 72 ASP cc_start: 0.7933 (m-30) cc_final: 0.7725 (m-30) REVERT: D 136 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.8033 (m90) REVERT: H 121 ILE cc_start: 0.6929 (mm) cc_final: 0.6212 (tt) REVERT: H 225 GLN cc_start: 0.6475 (mt0) cc_final: 0.5907 (tp-100) REVERT: I 132 ASP cc_start: 0.6910 (m-30) cc_final: 0.6678 (m-30) REVERT: L 72 THR cc_start: 0.7272 (OUTLIER) cc_final: 0.6914 (m) REVERT: M 141 ASN cc_start: 0.8613 (m-40) cc_final: 0.8379 (m-40) REVERT: N 112 LYS cc_start: 0.5273 (mptt) cc_final: 0.5054 (mmtt) REVERT: P 96 LYS cc_start: 0.8494 (mttt) cc_final: 0.8016 (mmtt) REVERT: Q 82 ASP cc_start: 0.8372 (p0) cc_final: 0.7991 (p0) REVERT: Q 106 GLU cc_start: 0.7255 (tp30) cc_final: 0.6937 (tp30) REVERT: T 89 ASP cc_start: 0.6848 (t70) cc_final: 0.6477 (t70) REVERT: V 113 GLU cc_start: 0.6368 (tm-30) cc_final: 0.6113 (tm-30) REVERT: X 87 GLU cc_start: 0.7075 (tp30) cc_final: 0.6836 (tp30) REVERT: X 91 ASN cc_start: 0.8137 (m-40) cc_final: 0.7782 (m110) REVERT: Z 13 MET cc_start: 0.7742 (tmm) cc_final: 0.7469 (tmm) REVERT: Z 74 MET cc_start: 0.7893 (mpp) cc_final: 0.7055 (mpp) REVERT: g 94 LYS cc_start: 0.6270 (ptpp) cc_final: 0.5627 (mmtp) REVERT: n 14 LYS cc_start: 0.8357 (mmmt) cc_final: 0.7860 (mtmt) REVERT: n 21 ARG cc_start: 0.6724 (tpt170) cc_final: 0.6134 (mtp-110) outliers start: 128 outliers final: 97 residues processed: 733 average time/residue: 0.7737 time to fit residues: 971.5112 Evaluate side-chains 734 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 635 time to evaluate : 4.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 194 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain O residue 31 ASP Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 89 MET Chi-restraints excluded: chain Q residue 127 LYS Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain V residue 18 HIS Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain X residue 30 CYS Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 99 GLU Chi-restraints excluded: chain Y residue 129 SER Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 51 THR Chi-restraints excluded: chain Z residue 55 ILE Chi-restraints excluded: chain Z residue 78 SER Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 107 VAL Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 62 GLU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain g residue 107 LYS Chi-restraints excluded: chain h residue 5 MET Chi-restraints excluded: chain h residue 174 VAL Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 142 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 150 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 560 optimal weight: 5.9990 chunk 381 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 500 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 574 optimal weight: 4.9990 chunk 465 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 343 optimal weight: 10.0000 chunk 603 optimal weight: 0.7980 chunk 169 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN C 147 ASN G 83 ASN K 132 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN S 62 GLN S 83 ASN T 72 GLN ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 GLN X 113 HIS j 41 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 88614 Z= 0.157 Angle : 0.528 10.811 129038 Z= 0.271 Chirality : 0.035 0.265 16020 Planarity : 0.004 0.054 9106 Dihedral : 22.811 179.770 36414 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.62 % Allowed : 16.50 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.65 (0.12), residues: 5104 helix: 1.23 (0.13), residues: 1668 sheet: -0.59 (0.17), residues: 917 loop : -1.55 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 82 HIS 0.004 0.001 HIS h 191 PHE 0.032 0.001 PHE c 79 TYR 0.022 0.001 TYR R 99 ARG 0.009 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 670 time to evaluate : 4.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.3825 (mptt) cc_final: 0.2337 (ttmt) REVERT: C 169 MET cc_start: 0.7784 (mtt) cc_final: 0.7575 (mtt) REVERT: D 72 ASP cc_start: 0.7934 (m-30) cc_final: 0.7713 (m-30) REVERT: D 136 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.7989 (m90) REVERT: H 121 ILE cc_start: 0.6921 (mm) cc_final: 0.6184 (tt) REVERT: H 225 GLN cc_start: 0.6533 (mt0) cc_final: 0.5947 (tp-100) REVERT: I 131 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6810 (pp20) REVERT: P 96 LYS cc_start: 0.8465 (mttt) cc_final: 0.8093 (mmtt) REVERT: Q 82 ASP cc_start: 0.8323 (p0) cc_final: 0.7978 (p0) REVERT: T 89 ASP cc_start: 0.6733 (t70) cc_final: 0.6353 (t70) REVERT: Z 13 MET cc_start: 0.7758 (tmm) cc_final: 0.7512 (tmm) REVERT: Z 74 MET cc_start: 0.7931 (mpp) cc_final: 0.7115 (mpp) REVERT: a 97 ILE cc_start: 0.7683 (mm) cc_final: 0.7447 (mt) REVERT: g 94 LYS cc_start: 0.6263 (ptpp) cc_final: 0.5603 (mmtp) REVERT: n 14 LYS cc_start: 0.8335 (mmmt) cc_final: 0.7838 (mtmt) REVERT: n 21 ARG cc_start: 0.6710 (tpt170) cc_final: 0.6160 (mtp-110) outliers start: 114 outliers final: 84 residues processed: 740 average time/residue: 0.7838 time to fit residues: 991.0717 Evaluate side-chains 730 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 645 time to evaluate : 4.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 194 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 106 ARG Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 127 LYS Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain V residue 18 HIS Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 50 PHE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain X residue 30 CYS Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 99 GLU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 129 SER Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 51 THR Chi-restraints excluded: chain Z residue 55 ILE Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 62 GLU Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain g residue 107 LYS Chi-restraints excluded: chain h residue 5 MET Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 142 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 150 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 226 optimal weight: 10.0000 chunk 605 optimal weight: 0.5980 chunk 132 optimal weight: 10.0000 chunk 394 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 673 optimal weight: 30.0000 chunk 559 optimal weight: 10.0000 chunk 311 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 222 optimal weight: 0.0470 chunk 353 optimal weight: 0.0670 overall best weight: 3.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN B 84 GLN C 147 ASN G 83 ASN H 110 ASN I 76 GLN J 165 GLN K 132 GLN L 7 ASN L 61 GLN M 141 ASN S 62 GLN ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 91 ASN j 41 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 88614 Z= 0.193 Angle : 0.531 10.660 129038 Z= 0.271 Chirality : 0.035 0.266 16020 Planarity : 0.004 0.065 9106 Dihedral : 22.767 179.937 36414 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.37 % Allowed : 16.63 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.56 (0.12), residues: 5104 helix: 1.33 (0.13), residues: 1665 sheet: -0.61 (0.17), residues: 917 loop : -1.47 (0.12), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 7 HIS 0.005 0.001 HIS h 191 PHE 0.023 0.001 PHE I 19 TYR 0.019 0.001 TYR L 78 ARG 0.010 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 666 time to evaluate : 4.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.3846 (mptt) cc_final: 0.2133 (ttmm) REVERT: C 89 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6059 (pt0) REVERT: C 169 MET cc_start: 0.7836 (mtt) cc_final: 0.7614 (mtt) REVERT: D 72 ASP cc_start: 0.7910 (m-30) cc_final: 0.7678 (m-30) REVERT: D 136 HIS cc_start: 0.8555 (OUTLIER) cc_final: 0.7934 (m90) REVERT: D 213 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8592 (tp) REVERT: D 248 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: E 4 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.5926 (pp30) REVERT: F 66 MET cc_start: 0.7508 (mmm) cc_final: 0.7280 (mmm) REVERT: F 251 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6878 (mt-10) REVERT: H 121 ILE cc_start: 0.6812 (mm) cc_final: 0.6071 (tt) REVERT: H 192 ILE cc_start: 0.8856 (mm) cc_final: 0.8419 (mt) REVERT: H 225 GLN cc_start: 0.6609 (mt0) cc_final: 0.5993 (tp-100) REVERT: I 72 PHE cc_start: 0.7903 (m-80) cc_final: 0.7653 (m-80) REVERT: N 112 LYS cc_start: 0.5218 (mptt) cc_final: 0.4367 (pttm) REVERT: P 96 LYS cc_start: 0.8526 (mttt) cc_final: 0.8109 (mmtt) REVERT: Q 82 ASP cc_start: 0.8349 (p0) cc_final: 0.8027 (p0) REVERT: Q 106 GLU cc_start: 0.7262 (tp30) cc_final: 0.6916 (tp30) REVERT: T 89 ASP cc_start: 0.6777 (t70) cc_final: 0.6442 (t70) REVERT: V 113 GLU cc_start: 0.6240 (tm-30) cc_final: 0.6013 (tm-30) REVERT: W 76 ASP cc_start: 0.7874 (t0) cc_final: 0.7510 (t0) REVERT: W 78 ILE cc_start: 0.8575 (mm) cc_final: 0.8213 (mt) REVERT: X 91 ASN cc_start: 0.8095 (m-40) cc_final: 0.7701 (m110) REVERT: Z 74 MET cc_start: 0.7948 (mpp) cc_final: 0.7081 (mpp) REVERT: a 97 ILE cc_start: 0.7831 (mm) cc_final: 0.7578 (mt) REVERT: b 37 LYS cc_start: 0.7928 (mtmm) cc_final: 0.7521 (mtmm) REVERT: b 54 SER cc_start: 0.7835 (OUTLIER) cc_final: 0.7571 (t) REVERT: c 9 HIS cc_start: 0.6909 (OUTLIER) cc_final: 0.5971 (p-80) REVERT: g 94 LYS cc_start: 0.6124 (ptpp) cc_final: 0.5388 (mmtp) REVERT: h 142 VAL cc_start: 0.6647 (OUTLIER) cc_final: 0.6324 (p) REVERT: n 14 LYS cc_start: 0.8350 (mmmt) cc_final: 0.7840 (mtmt) REVERT: n 21 ARG cc_start: 0.6740 (tpt170) cc_final: 0.6160 (mtp-110) outliers start: 147 outliers final: 105 residues processed: 762 average time/residue: 0.8517 time to fit residues: 1123.2279 Evaluate side-chains 753 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 640 time to evaluate : 4.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 194 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 132 GLN Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain O residue 31 ASP Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 89 MET Chi-restraints excluded: chain Q residue 127 LYS Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain V residue 18 HIS Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 50 PHE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain X residue 30 CYS Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 129 SER Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 51 THR Chi-restraints excluded: chain Z residue 55 ILE Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain c residue 9 HIS Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 62 GLU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain g residue 107 LYS Chi-restraints excluded: chain h residue 5 MET Chi-restraints excluded: chain h residue 111 VAL Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 174 VAL Chi-restraints excluded: chain h residue 176 VAL Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 142 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 150 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 649 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 383 optimal weight: 10.0000 chunk 491 optimal weight: 8.9990 chunk 381 optimal weight: 9.9990 chunk 566 optimal weight: 9.9990 chunk 376 optimal weight: 6.9990 chunk 670 optimal weight: 1.9990 chunk 419 optimal weight: 6.9990 chunk 408 optimal weight: 0.9990 chunk 309 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN C 147 ASN F 179 ASN G 83 ASN I 76 GLN J 165 GLN L 7 ASN L 61 GLN M 141 ASN S 62 GLN S 83 ASN U 12 GLN j 41 ASN j 68 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 88614 Z= 0.252 Angle : 0.572 11.246 129038 Z= 0.291 Chirality : 0.037 0.276 16020 Planarity : 0.004 0.058 9106 Dihedral : 22.795 179.721 36414 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.53 % Allowed : 17.27 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.63 (0.12), residues: 5104 helix: 1.23 (0.13), residues: 1668 sheet: -0.66 (0.17), residues: 923 loop : -1.49 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 82 HIS 0.006 0.001 HIS T 135 PHE 0.025 0.002 PHE c 79 TYR 0.019 0.002 TYR R 99 ARG 0.009 0.000 ARG K 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 662 time to evaluate : 4.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.4176 (mptt) cc_final: 0.2410 (ttmm) REVERT: C 89 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6150 (pt0) REVERT: C 169 MET cc_start: 0.7798 (mtt) cc_final: 0.7596 (mtt) REVERT: D 136 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.7918 (m90) REVERT: D 213 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8580 (tp) REVERT: D 248 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: E 4 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.5951 (pp30) REVERT: F 251 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6942 (mt-10) REVERT: H 121 ILE cc_start: 0.6840 (mm) cc_final: 0.6072 (tt) REVERT: H 192 ILE cc_start: 0.8838 (mm) cc_final: 0.8412 (mt) REVERT: H 225 GLN cc_start: 0.6656 (mt0) cc_final: 0.6041 (tp-100) REVERT: N 46 GLN cc_start: 0.4078 (mm110) cc_final: 0.3870 (mm-40) REVERT: N 112 LYS cc_start: 0.5322 (mptt) cc_final: 0.4459 (pttm) REVERT: P 96 LYS cc_start: 0.8577 (mttt) cc_final: 0.8125 (mmtt) REVERT: Q 82 ASP cc_start: 0.8352 (p0) cc_final: 0.7994 (p0) REVERT: T 89 ASP cc_start: 0.6923 (t70) cc_final: 0.6547 (t70) REVERT: T 144 ARG cc_start: 0.4824 (ptm160) cc_final: 0.4168 (ptp-170) REVERT: V 113 GLU cc_start: 0.6203 (tm-30) cc_final: 0.5950 (tm-30) REVERT: W 76 ASP cc_start: 0.7912 (t0) cc_final: 0.7685 (t0) REVERT: W 78 ILE cc_start: 0.8584 (mm) cc_final: 0.8264 (mt) REVERT: Z 74 MET cc_start: 0.7933 (mpp) cc_final: 0.7016 (mpp) REVERT: b 37 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7521 (mtmm) REVERT: b 54 SER cc_start: 0.7860 (OUTLIER) cc_final: 0.7584 (t) REVERT: c 9 HIS cc_start: 0.7064 (OUTLIER) cc_final: 0.6232 (p-80) REVERT: g 94 LYS cc_start: 0.5984 (ptpp) cc_final: 0.5188 (mmtp) REVERT: n 14 LYS cc_start: 0.8317 (mmmt) cc_final: 0.7797 (mtmt) REVERT: n 21 ARG cc_start: 0.6587 (tpt170) cc_final: 0.5965 (mtp-110) outliers start: 154 outliers final: 117 residues processed: 763 average time/residue: 0.7746 time to fit residues: 1011.8260 Evaluate side-chains 765 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 641 time to evaluate : 4.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 194 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 89 MET Chi-restraints excluded: chain Q residue 127 LYS Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain V residue 18 HIS Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 50 PHE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain X residue 30 CYS Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 129 SER Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 51 THR Chi-restraints excluded: chain Z residue 55 ILE Chi-restraints excluded: chain Z residue 78 SER Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain c residue 9 HIS Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 62 GLU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain g residue 107 LYS Chi-restraints excluded: chain h residue 5 MET Chi-restraints excluded: chain h residue 111 VAL Chi-restraints excluded: chain h residue 174 VAL Chi-restraints excluded: chain h residue 176 VAL Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 142 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 150 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 415 optimal weight: 0.9990 chunk 267 optimal weight: 8.9990 chunk 400 optimal weight: 9.9990 chunk 202 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 426 optimal weight: 7.9990 chunk 457 optimal weight: 4.9990 chunk 331 optimal weight: 8.9990 chunk 62 optimal weight: 30.0000 chunk 527 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN C 147 ASN F 179 ASN G 83 ASN J 165 GLN L 7 ASN L 61 GLN M 141 ASN S 62 GLN S 83 ASN U 12 GLN ** Z 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 41 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 88614 Z= 0.195 Angle : 0.545 12.207 129038 Z= 0.278 Chirality : 0.036 0.276 16020 Planarity : 0.004 0.056 9106 Dihedral : 22.796 179.805 36414 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.24 % Allowed : 18.16 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.55 (0.12), residues: 5104 helix: 1.32 (0.13), residues: 1663 sheet: -0.62 (0.17), residues: 921 loop : -1.45 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 82 HIS 0.005 0.001 HIS h 191 PHE 0.021 0.001 PHE X 50 TYR 0.020 0.001 TYR R 99 ARG 0.011 0.000 ARG d 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 655 time to evaluate : 4.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.4147 (mptt) cc_final: 0.3362 (mttm) REVERT: C 89 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6109 (pt0) REVERT: C 169 MET cc_start: 0.7773 (mtt) cc_final: 0.7556 (mtt) REVERT: D 136 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.7979 (m90) REVERT: D 213 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8593 (tp) REVERT: D 248 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: E 4 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.5933 (pp30) REVERT: F 19 MET cc_start: 0.8184 (mtm) cc_final: 0.7798 (mtm) REVERT: F 251 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6890 (mt-10) REVERT: H 121 ILE cc_start: 0.6857 (mm) cc_final: 0.6063 (tt) REVERT: H 192 ILE cc_start: 0.8854 (mm) cc_final: 0.8445 (mt) REVERT: H 225 GLN cc_start: 0.6721 (mt0) cc_final: 0.6072 (tp-100) REVERT: P 96 LYS cc_start: 0.8561 (mttt) cc_final: 0.8125 (mmtt) REVERT: Q 82 ASP cc_start: 0.8321 (p0) cc_final: 0.8009 (p0) REVERT: Q 106 GLU cc_start: 0.7256 (tp30) cc_final: 0.6837 (tp30) REVERT: T 89 ASP cc_start: 0.6891 (t70) cc_final: 0.6507 (t70) REVERT: W 76 ASP cc_start: 0.7906 (t0) cc_final: 0.7674 (t0) REVERT: W 78 ILE cc_start: 0.8571 (mm) cc_final: 0.8261 (mt) REVERT: Z 74 MET cc_start: 0.7922 (mpp) cc_final: 0.7014 (mpp) REVERT: a 89 GLN cc_start: 0.6765 (mp10) cc_final: 0.6503 (mp10) REVERT: b 37 LYS cc_start: 0.7919 (mtmm) cc_final: 0.7521 (mtmm) REVERT: b 54 SER cc_start: 0.7782 (OUTLIER) cc_final: 0.7498 (t) REVERT: c 9 HIS cc_start: 0.7032 (OUTLIER) cc_final: 0.6208 (p-80) REVERT: g 94 LYS cc_start: 0.5986 (ptpp) cc_final: 0.5194 (mmtp) REVERT: g 107 LYS cc_start: 0.3569 (OUTLIER) cc_final: 0.3354 (ttpt) REVERT: j 88 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7301 (mtp180) REVERT: n 14 LYS cc_start: 0.8331 (mmmt) cc_final: 0.7780 (mtmt) REVERT: n 21 ARG cc_start: 0.6681 (tpt170) cc_final: 0.6055 (mtp-110) outliers start: 141 outliers final: 115 residues processed: 746 average time/residue: 0.8244 time to fit residues: 1055.4298 Evaluate side-chains 764 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 641 time to evaluate : 4.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 194 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 89 MET Chi-restraints excluded: chain Q residue 127 LYS Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 51 ASP Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain V residue 18 HIS Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 50 PHE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain X residue 30 CYS Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 129 SER Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 51 THR Chi-restraints excluded: chain Z residue 55 ILE Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain a residue 44 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain c residue 9 HIS Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 62 GLU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain g residue 107 LYS Chi-restraints excluded: chain h residue 5 MET Chi-restraints excluded: chain h residue 111 VAL Chi-restraints excluded: chain h residue 174 VAL Chi-restraints excluded: chain h residue 176 VAL Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 142 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 150 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 610 optimal weight: 6.9990 chunk 642 optimal weight: 10.0000 chunk 586 optimal weight: 9.9990 chunk 625 optimal weight: 6.9990 chunk 376 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 490 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 564 optimal weight: 4.9990 chunk 591 optimal weight: 3.9990 chunk 622 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN C 147 ASN F 179 ASN G 83 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN L 61 GLN M 141 ASN S 62 GLN T 73 ASN U 12 GLN ** Z 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN j 41 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 88614 Z= 0.233 Angle : 0.568 12.388 129038 Z= 0.289 Chirality : 0.037 0.278 16020 Planarity : 0.004 0.056 9106 Dihedral : 22.810 179.907 36414 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.49 % Allowed : 18.00 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.62 (0.12), residues: 5104 helix: 1.28 (0.13), residues: 1655 sheet: -0.71 (0.17), residues: 928 loop : -1.48 (0.12), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 7 HIS 0.005 0.001 HIS T 135 PHE 0.023 0.002 PHE c 79 TYR 0.023 0.001 TYR R 99 ARG 0.006 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 653 time to evaluate : 4.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.4426 (mptt) cc_final: 0.3606 (mttm) REVERT: C 89 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6126 (pt0) REVERT: C 169 MET cc_start: 0.7792 (mtt) cc_final: 0.7590 (mtt) REVERT: D 136 HIS cc_start: 0.8603 (OUTLIER) cc_final: 0.7959 (m90) REVERT: D 213 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8566 (tp) REVERT: D 248 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: E 4 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.5973 (pp30) REVERT: F 251 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6944 (mt-10) REVERT: H 121 ILE cc_start: 0.6849 (mm) cc_final: 0.6071 (tt) REVERT: H 192 ILE cc_start: 0.8855 (mm) cc_final: 0.8443 (mt) REVERT: H 225 GLN cc_start: 0.6686 (mt0) cc_final: 0.6040 (tp-100) REVERT: P 96 LYS cc_start: 0.8577 (mttt) cc_final: 0.8132 (mmtt) REVERT: Q 82 ASP cc_start: 0.8332 (p0) cc_final: 0.7997 (p0) REVERT: Q 106 GLU cc_start: 0.7225 (tp30) cc_final: 0.6860 (tp30) REVERT: T 89 ASP cc_start: 0.6941 (t70) cc_final: 0.6531 (t70) REVERT: W 76 ASP cc_start: 0.7963 (t0) cc_final: 0.7709 (t0) REVERT: W 78 ILE cc_start: 0.8604 (mm) cc_final: 0.8309 (mt) REVERT: Z 74 MET cc_start: 0.7905 (mpp) cc_final: 0.7007 (mpp) REVERT: b 37 LYS cc_start: 0.7897 (mtmm) cc_final: 0.7497 (mtmm) REVERT: b 54 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7505 (t) REVERT: c 9 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6349 (p-80) REVERT: d 35 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6066 (mtp) REVERT: g 94 LYS cc_start: 0.5851 (ptpp) cc_final: 0.5079 (mmtp) REVERT: g 107 LYS cc_start: 0.3662 (OUTLIER) cc_final: 0.3453 (ttpt) REVERT: n 14 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7770 (mtmt) outliers start: 152 outliers final: 125 residues processed: 753 average time/residue: 0.7829 time to fit residues: 1006.9689 Evaluate side-chains 774 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 640 time to evaluate : 4.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 194 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 127 LYS Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 51 ASP Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain V residue 18 HIS Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 50 PHE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain X residue 30 CYS Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 129 SER Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 51 THR Chi-restraints excluded: chain Z residue 55 ILE Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain a residue 44 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain c residue 9 HIS Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain d residue 62 GLU Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain g residue 107 LYS Chi-restraints excluded: chain h residue 5 MET Chi-restraints excluded: chain h residue 111 VAL Chi-restraints excluded: chain h residue 174 VAL Chi-restraints excluded: chain h residue 176 VAL Chi-restraints excluded: chain h residue 196 ASN Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 142 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 150 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 410 optimal weight: 1.9990 chunk 661 optimal weight: 10.0000 chunk 403 optimal weight: 0.9980 chunk 313 optimal weight: 2.9990 chunk 459 optimal weight: 5.9990 chunk 693 optimal weight: 20.0000 chunk 638 optimal weight: 20.0000 chunk 552 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 426 optimal weight: 8.9990 chunk 338 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 GLN L 7 ASN L 61 GLN M 141 ASN S 83 ASN U 12 GLN ** Z 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN j 41 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 88614 Z= 0.223 Angle : 0.565 12.831 129038 Z= 0.288 Chirality : 0.037 0.283 16020 Planarity : 0.004 0.055 9106 Dihedral : 22.814 179.880 36414 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.28 % Allowed : 18.46 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.59 (0.12), residues: 5104 helix: 1.30 (0.13), residues: 1651 sheet: -0.64 (0.17), residues: 928 loop : -1.48 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 82 HIS 0.005 0.001 HIS h 191 PHE 0.026 0.001 PHE I 19 TYR 0.021 0.001 TYR R 99 ARG 0.012 0.000 ARG Q 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 653 time to evaluate : 4.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.4420 (mptt) cc_final: 0.3595 (mttm) REVERT: C 89 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6128 (pt0) REVERT: D 136 HIS cc_start: 0.8580 (OUTLIER) cc_final: 0.7942 (m90) REVERT: D 213 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8595 (tp) REVERT: D 248 TYR cc_start: 0.9033 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: E 4 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.5924 (pp30) REVERT: F 182 MET cc_start: 0.7227 (ttt) cc_final: 0.7027 (ttm) REVERT: H 121 ILE cc_start: 0.6864 (mm) cc_final: 0.6079 (tt) REVERT: H 192 ILE cc_start: 0.8843 (mm) cc_final: 0.8420 (mt) REVERT: H 225 GLN cc_start: 0.6697 (mt0) cc_final: 0.6043 (tp-100) REVERT: P 96 LYS cc_start: 0.8577 (mttt) cc_final: 0.8126 (mmtt) REVERT: Q 82 ASP cc_start: 0.8320 (p0) cc_final: 0.7983 (p0) REVERT: T 89 ASP cc_start: 0.6943 (t70) cc_final: 0.6513 (t70) REVERT: W 11 LEU cc_start: 0.8663 (pt) cc_final: 0.8391 (pp) REVERT: W 76 ASP cc_start: 0.7974 (t0) cc_final: 0.7694 (t0) REVERT: W 78 ILE cc_start: 0.8592 (mm) cc_final: 0.8300 (mt) REVERT: Z 74 MET cc_start: 0.7909 (mpp) cc_final: 0.7008 (mpp) REVERT: b 37 LYS cc_start: 0.7889 (mtmm) cc_final: 0.7491 (mtmm) REVERT: b 54 SER cc_start: 0.7728 (OUTLIER) cc_final: 0.7418 (t) REVERT: c 9 HIS cc_start: 0.7126 (OUTLIER) cc_final: 0.6333 (p-80) REVERT: d 35 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.6044 (mtt) REVERT: g 94 LYS cc_start: 0.5853 (ptpp) cc_final: 0.5080 (mmtp) REVERT: g 132 MET cc_start: 0.5918 (mtt) cc_final: 0.5674 (mtt) REVERT: j 88 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7274 (mtp180) REVERT: n 14 LYS cc_start: 0.8343 (mmmt) cc_final: 0.7772 (mtmt) outliers start: 143 outliers final: 128 residues processed: 745 average time/residue: 0.7976 time to fit residues: 1017.9139 Evaluate side-chains 778 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 642 time to evaluate : 4.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 194 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 89 MET Chi-restraints excluded: chain Q residue 127 LYS Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 84 TYR Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 51 ASP Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain V residue 18 HIS Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 50 PHE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain X residue 30 CYS Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 129 SER Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 51 THR Chi-restraints excluded: chain Z residue 55 ILE Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain a residue 44 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain c residue 9 HIS Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain d residue 62 GLU Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain h residue 5 MET Chi-restraints excluded: chain h residue 111 VAL Chi-restraints excluded: chain h residue 174 VAL Chi-restraints excluded: chain h residue 176 VAL Chi-restraints excluded: chain h residue 196 ASN Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 142 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 150 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 438 optimal weight: 2.9990 chunk 588 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 509 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 553 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 567 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN L 7 ASN L 61 GLN M 141 ASN T 73 ASN T 76 GLN U 12 GLN ** Z 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 HIS j 41 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.101740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.076562 restraints weight = 192261.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.075709 restraints weight = 160919.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.077037 restraints weight = 130875.799| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 88614 Z= 0.339 Angle : 0.655 12.896 129038 Z= 0.332 Chirality : 0.041 0.307 16020 Planarity : 0.005 0.056 9106 Dihedral : 22.911 179.805 36414 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.33 % Allowed : 18.32 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.87 (0.12), residues: 5104 helix: 0.99 (0.13), residues: 1669 sheet: -0.80 (0.17), residues: 910 loop : -1.59 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP T 82 HIS 0.007 0.001 HIS T 135 PHE 0.042 0.002 PHE j 138 TYR 0.023 0.002 TYR R 99 ARG 0.013 0.001 ARG Q 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16216.08 seconds wall clock time: 288 minutes 2.13 seconds (17282.13 seconds total)