Starting phenix.real_space_refine (version: 1.21rc1) on Tue Aug 22 07:49:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/08_2023/6khi_9989_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/08_2023/6khi_9989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/08_2023/6khi_9989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/08_2023/6khi_9989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/08_2023/6khi_9989_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6khi_9989/08_2023/6khi_9989_updated.pdb" } resolution = 3.0 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 ------------------------------------------------------------------------------- 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= 0.007 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 Fe 14 7.16 5 P 6 5.49 5 S 184 5.16 5 C 21526 2.51 5 N 5162 2.21 5 O 5743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 2": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 449": "OE1" <-> "OE2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 123": "NH1" <-> "NH2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F ARG 388": "NH1" <-> "NH2" Residue "F ARG 459": "NH1" <-> "NH2" Residue "F GLU 464": "OE1" <-> "OE2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 512": "OE1" <-> "OE2" Residue "F ARG 599": "NH1" <-> "NH2" Residue "F ARG 634": "NH1" <-> "NH2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G ARG 166": "NH1" <-> "NH2" Residue "G ARG 167": "NH1" <-> "NH2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "H ARG 226": "NH1" <-> "NH2" Residue "H GLU 241": "OE1" <-> "OE2" Residue "H ARG 277": "NH1" <-> "NH2" Residue "H ARG 330": "NH1" <-> "NH2" Residue "H ARG 352": "NH1" <-> "NH2" Residue "I ARG 33": "NH1" <-> "NH2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I GLU 133": "OE1" <-> "OE2" Residue "I ARG 179": "NH1" <-> "NH2" Residue "J ARG 90": "NH1" <-> "NH2" Residue "J GLU 166": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K ARG 100": "NH1" <-> "NH2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K ARG 151": "NH1" <-> "NH2" Residue "K ARG 182": "NH1" <-> "NH2" Residue "L GLU 6": "OE1" <-> "OE2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M GLU 55": "OE1" <-> "OE2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "M ARG 72": "NH1" <-> "NH2" Residue "M ARG 82": "NH1" <-> "NH2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "M ARG 99": "NH1" <-> "NH2" Residue "N ARG 32": "NH1" <-> "NH2" Residue "N ARG 36": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N GLU 112": "OE1" <-> "OE2" Residue "N ARG 136": "NH1" <-> "NH2" Residue "O ARG 44": "NH1" <-> "NH2" Residue "V GLU 50": "OE1" <-> "OE2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V GLU 72": "OE1" <-> "OE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "V GLU 115": "OE1" <-> "OE2" Residue "1 GLU 31": "OE1" <-> "OE2" Residue "1 GLU 72": "OE1" <-> "OE2" Residue "1 ARG 84": "NH1" <-> "NH2" Residue "1 GLU 94": "OE1" <-> "OE2" Residue "1 GLU 95": "OE1" <-> "OE2" Residue "1 GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 32635 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2821 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Chain: "B" Number of atoms: 3724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3724 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 18, 'TRANS': 473} Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 971 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3897 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 26, 'TRANS': 477} Chain: "E" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 775 Classifications: {'peptide': 100} Link IDs: {'TRANS': 99} Chain: "F" Number of atoms: 4945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 4945 Classifications: {'peptide': 641} Link IDs: {'PTRANS': 32, 'TRANS': 608} Chain breaks: 2 Chain: "G" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1278 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3177 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain: "I" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1537 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain: "J" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1307 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 11, 'TRANS': 148} Chain: "K" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1590 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 20, 'TRANS': 184} Chain: "L" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "N" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 11, 'TRANS': 136} Chain: "O" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "P" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 321 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 333 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "S" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 469 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "V" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 838 Classifications: {'peptide': 109} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "1" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 756 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 124 Unusual residues: {'DGD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'LHG': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "D" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'BCR': 2, 'SQD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'LHG': 3, 'LMG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 41 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'LHG': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'SQD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22426 SG CYS I 103 51.247 147.432 125.066 1.00 26.51 S ATOM 22470 SG CYS I 109 46.922 151.988 124.714 1.00 32.39 S ATOM 22175 SG CYS I 73 46.055 146.638 121.137 1.00 29.12 S ATOM 22451 SG CYS I 106 50.504 150.648 119.533 1.00 28.97 S ATOM 22122 SG CYS I 66 36.063 154.706 125.280 1.00 42.91 S ATOM 22144 SG CYS I 69 40.935 150.705 125.903 1.00 35.01 S ATOM 22103 SG CYS I 63 38.256 153.294 131.116 1.00 46.30 S ATOM 22504 SG CYS I 113 41.754 156.985 127.101 1.00 38.42 S ATOM 25530 SG CYS K 148 57.799 145.760 118.845 1.00 30.02 S ATOM 24806 SG CYS K 53 62.990 142.480 120.310 1.00 30.13 S ATOM 24800 SG CYS K 52 61.997 143.616 114.451 1.00 33.10 S ATOM 25304 SG CYS K 117 57.766 139.725 117.520 1.00 26.14 S ATOM 31484 SG CYS 1 41 32.927 160.609 122.910 1.00 83.69 S ATOM 31515 SG CYS 1 46 30.656 158.601 125.006 1.00 81.81 S ATOM 31534 SG CYS 1 49 27.912 161.206 121.565 1.00 94.03 S ATOM 31764 SG CYS 1 79 29.354 164.549 121.962 1.00100.16 S Time building chain proxies: 15.93, per 1000 atoms: 0.49 Number of scatterers: 32635 At special positions: 0 Unit cell: (168.48, 203.84, 172.64, 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) Fe 14 26.01 S 184 16.00 P 6 15.00 O 5743 8.00 N 5162 7.00 C 21526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.50 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 1 101 " pdb="FE2 FES 1 101 " - pdb=" SG CYS 1 49 " pdb="FE1 FES 1 101 " - pdb=" SG CYS 1 41 " pdb="FE1 FES 1 101 " - pdb=" SG CYS 1 46 " pdb="FE2 FES 1 101 " - pdb=" SG CYS 1 79 " pdb=" SF4 I 202 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 103 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 73 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 106 " pdb=" SF4 I 203 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 63 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 69 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 113 " pdb=" SF4 K 301 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 52 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 117 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 53 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 148 " Number of angles added : 42 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 161 helices and 14 sheets defined 52.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 Processing helix chain 'A' and resid 22 through 59 Proline residue: A 31 - end of helix removed outlier: 4.228A pdb=" N MET A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 56 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 85 Proline residue: A 76 - end of helix removed outlier: 4.125A pdb=" N LYS A 82 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 84 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 Proline residue: A 103 - end of helix Proline residue: A 109 - end of helix removed outlier: 4.401A pdb=" N TYR A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 151 removed outlier: 3.836A pdb=" N ILE A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix removed outlier: 4.554A pdb=" N LEU A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.668A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 213 through 226 removed outlier: 3.811A pdb=" N LEU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 275 removed outlier: 3.891A pdb=" N TYR A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 Processing helix chain 'A' and resid 300 through 329 Processing helix chain 'A' and resid 341 through 344 No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 348 through 365 Processing helix chain 'B' and resid 15 through 34 removed outlier: 3.847A pdb=" N THR B 19 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE B 20 " --> pdb=" O PRO B 17 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR B 24 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE B 34 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.889A pdb=" N ARG B 41 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 62 removed outlier: 3.711A pdb=" N ILE B 59 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Proline residue: B 60 - end of helix Processing helix chain 'B' and resid 78 through 97 Processing helix chain 'B' and resid 101 through 104 No H-bonds generated for 'chain 'B' and resid 101 through 104' Processing helix chain 'B' and resid 110 through 127 removed outlier: 3.870A pdb=" N ILE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 150 Processing helix chain 'B' and resid 157 through 187 removed outlier: 3.675A pdb=" N ILE B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 208 through 223 removed outlier: 3.666A pdb=" N PHE B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 238 removed outlier: 5.374A pdb=" N GLN B 230 " --> pdb=" O PRO B 227 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TRP B 231 " --> pdb=" O PHE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 4.182A pdb=" N TYR B 236 " --> pdb=" O PRO B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 263 removed outlier: 4.232A pdb=" N SER B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 290 Processing helix chain 'B' and resid 299 through 320 removed outlier: 3.588A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 353 removed outlier: 3.833A pdb=" N PHE B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 370 through 384 Processing helix chain 'B' and resid 390 through 403 removed outlier: 4.396A pdb=" N GLY B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 433 removed outlier: 3.905A pdb=" N TYR B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL B 428 " --> pdb=" O TYR B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 445 No H-bonds generated for 'chain 'B' and resid 442 through 445' Processing helix chain 'B' and resid 457 through 476 removed outlier: 4.298A pdb=" N ALA B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLY B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 486 Processing helix chain 'C' and resid 19 through 42 removed outlier: 3.735A pdb=" N GLY C 24 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Proline residue: C 33 - end of helix Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 74 through 98 removed outlier: 3.970A pdb=" N ALA C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU C 79 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) Proline residue: C 93 - end of helix removed outlier: 3.615A pdb=" N PHE C 98 " --> pdb=" O TRP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 125 Processing helix chain 'D' and resid 6 through 18 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 32 through 56 removed outlier: 3.848A pdb=" N TRP D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 108 removed outlier: 4.021A pdb=" N TRP D 107 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Proline residue: D 108 - end of helix Processing helix chain 'D' and resid 113 through 132 removed outlier: 4.403A pdb=" N GLY D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE D 128 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 130 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 removed outlier: 4.312A pdb=" N GLU D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 162 through 188 removed outlier: 3.785A pdb=" N GLY D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 176 " --> pdb=" O TYR D 172 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE D 179 " --> pdb=" O GLY D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 210 through 225 removed outlier: 3.933A pdb=" N LYS D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 238 No H-bonds generated for 'chain 'D' and resid 235 through 238' Processing helix chain 'D' and resid 244 through 250 removed outlier: 3.832A pdb=" N LEU D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 264 No H-bonds generated for 'chain 'D' and resid 261 through 264' Processing helix chain 'D' and resid 271 through 296 removed outlier: 3.851A pdb=" N LYS D 276 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 303 through 322 removed outlier: 4.169A pdb=" N ILE D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY D 315 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N PHE D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL D 317 " --> pdb=" O HIS D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 357 removed outlier: 4.166A pdb=" N GLY D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 371 No H-bonds generated for 'chain 'D' and resid 368 through 371' Processing helix chain 'D' and resid 374 through 386 Processing helix chain 'D' and resid 393 through 406 removed outlier: 3.826A pdb=" N ALA D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 441 removed outlier: 4.066A pdb=" N GLY D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) Proline residue: D 431 - end of helix removed outlier: 4.076A pdb=" N LEU D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 479 Proline residue: D 473 - end of helix Processing helix chain 'D' and resid 481 through 483 No H-bonds generated for 'chain 'D' and resid 481 through 483' Processing helix chain 'D' and resid 485 through 498 removed outlier: 5.421A pdb=" N ALA D 490 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR D 491 " --> pdb=" O ILE D 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 18 Processing helix chain 'E' and resid 27 through 51 removed outlier: 3.665A pdb=" N LEU E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 87 removed outlier: 3.668A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'F' and resid 3 through 6 No H-bonds generated for 'chain 'F' and resid 3 through 6' Processing helix chain 'F' and resid 8 through 27 removed outlier: 3.680A pdb=" N ILE F 11 " --> pdb=" O ALA F 8 " (cutoff:3.500A) Proline residue: F 12 - end of helix Proline residue: F 15 - end of helix removed outlier: 4.050A pdb=" N ILE F 21 " --> pdb=" O GLY F 18 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL F 22 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLY F 23 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE F 27 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 33 No H-bonds generated for 'chain 'F' and resid 30 through 33' Processing helix chain 'F' and resid 37 through 63 removed outlier: 4.288A pdb=" N GLY F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR F 57 " --> pdb=" O GLY F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 117 removed outlier: 3.969A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N HIS F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 139 removed outlier: 3.782A pdb=" N LEU F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 162 removed outlier: 4.304A pdb=" N TRP F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 199 removed outlier: 3.811A pdb=" N GLY F 185 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLY F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU F 191 " --> pdb=" O PHE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 216 removed outlier: 4.118A pdb=" N ASP F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 240 removed outlier: 4.120A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Proline residue: F 237 - end of helix Processing helix chain 'F' and resid 250 through 255 removed outlier: 3.740A pdb=" N MET F 254 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU F 255 " --> pdb=" O PRO F 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 250 through 255' Processing helix chain 'F' and resid 258 through 266 removed outlier: 3.892A pdb=" N HIS F 265 " --> pdb=" O SER F 261 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 279 removed outlier: 4.263A pdb=" N GLY F 273 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL F 274 " --> pdb=" O ALA F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 284 No H-bonds generated for 'chain 'F' and resid 281 through 284' Processing helix chain 'F' and resid 288 through 308 Processing helix chain 'F' and resid 317 through 335 Processing helix chain 'F' and resid 339 through 348 Processing helix chain 'F' and resid 353 through 368 removed outlier: 3.885A pdb=" N LEU F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 383 No H-bonds generated for 'chain 'F' and resid 381 through 383' Processing helix chain 'F' and resid 387 through 390 No H-bonds generated for 'chain 'F' and resid 387 through 390' Processing helix chain 'F' and resid 392 through 402 removed outlier: 4.981A pdb=" N GLY F 401 " --> pdb=" O THR F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 427 removed outlier: 3.776A pdb=" N GLU F 419 " --> pdb=" O TRP F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 454 removed outlier: 4.208A pdb=" N LEU F 434 " --> pdb=" O ALA F 430 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU F 437 " --> pdb=" O LEU F 433 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY F 440 " --> pdb=" O TRP F 436 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 492 Proline residue: F 489 - end of helix Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'F' and resid 500 through 504 Processing helix chain 'F' and resid 510 through 514 Processing helix chain 'F' and resid 532 through 555 removed outlier: 3.971A pdb=" N SER F 539 " --> pdb=" O ILE F 535 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY F 544 " --> pdb=" O SER F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 568 Processing helix chain 'F' and resid 570 through 577 Processing helix chain 'F' and resid 579 through 588 removed outlier: 3.548A pdb=" N PHE F 582 " --> pdb=" O LYS F 579 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP F 583 " --> pdb=" O TRP F 580 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU F 584 " --> pdb=" O TYR F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 619 removed outlier: 4.473A pdb=" N VAL F 609 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP F 610 " --> pdb=" O TYR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 628 through 630 No H-bonds generated for 'chain 'F' and resid 628 through 630' Processing helix chain 'F' and resid 635 through 654 removed outlier: 3.823A pdb=" N SER F 653 " --> pdb=" O PHE F 649 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 654 " --> pdb=" O VAL F 650 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 27 removed outlier: 3.945A pdb=" N THR G 11 " --> pdb=" O THR G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 52 removed outlier: 3.979A pdb=" N GLY G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 70 through 76 Processing helix chain 'G' and resid 99 through 115 Processing helix chain 'G' and resid 131 through 140 removed outlier: 3.913A pdb=" N PHE G 140 " --> pdb=" O GLY G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 164 removed outlier: 3.970A pdb=" N SER G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 57 removed outlier: 3.704A pdb=" N GLU H 56 " --> pdb=" O GLU H 52 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 No H-bonds generated for 'chain 'H' and resid 60 through 63' Processing helix chain 'H' and resid 76 through 90 Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 96 through 125 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 130 through 148 removed outlier: 4.223A pdb=" N PHE H 135 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ARG H 138 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU H 139 " --> pdb=" O ARG H 136 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR H 140 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA H 147 " --> pdb=" O LEU H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 191 removed outlier: 4.652A pdb=" N VAL H 173 " --> pdb=" O TYR H 170 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N THR H 174 " --> pdb=" O GLY H 171 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS H 175 " --> pdb=" O TRP H 172 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU H 184 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Proline residue: H 185 - end of helix removed outlier: 3.836A pdb=" N GLU H 191 " --> pdb=" O ASP H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 204 Processing helix chain 'H' and resid 212 through 218 Processing helix chain 'H' and resid 222 through 224 No H-bonds generated for 'chain 'H' and resid 222 through 224' Processing helix chain 'H' and resid 258 through 282 removed outlier: 3.551A pdb=" N VAL H 273 " --> pdb=" O MET H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 297 Processing helix chain 'H' and resid 377 through 385 Processing helix chain 'I' and resid 4 through 29 Processing helix chain 'I' and resid 41 through 43 No H-bonds generated for 'chain 'I' and resid 41 through 43' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 108 through 111 No H-bonds generated for 'chain 'I' and resid 108 through 111' Processing helix chain 'I' and resid 132 through 134 No H-bonds generated for 'chain 'I' and resid 132 through 134' Processing helix chain 'I' and resid 184 through 192 Processing helix chain 'J' and resid 46 through 54 Processing helix chain 'J' and resid 119 through 128 Processing helix chain 'J' and resid 162 through 164 No H-bonds generated for 'chain 'J' and resid 162 through 164' Processing helix chain 'K' and resid 26 through 40 Processing helix chain 'K' and resid 52 through 61 removed outlier: 3.818A pdb=" N ALA K 59 " --> pdb=" O GLU K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 70 No H-bonds generated for 'chain 'K' and resid 68 through 70' Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing helix chain 'K' and resid 94 through 103 Processing helix chain 'K' and resid 116 through 119 No H-bonds generated for 'chain 'K' and resid 116 through 119' Processing helix chain 'K' and resid 122 through 124 No H-bonds generated for 'chain 'K' and resid 122 through 124' Processing helix chain 'K' and resid 135 through 137 No H-bonds generated for 'chain 'K' and resid 135 through 137' Processing helix chain 'K' and resid 152 through 166 Processing helix chain 'L' and resid 6 through 21 Processing helix chain 'L' and resid 23 through 34 Processing helix chain 'L' and resid 41 through 53 Processing helix chain 'L' and resid 55 through 64 Proline residue: L 63 - end of helix Processing helix chain 'M' and resid 45 through 59 Processing helix chain 'M' and resid 67 through 87 Processing helix chain 'N' and resid 8 through 16 Processing helix chain 'N' and resid 31 through 40 removed outlier: 3.593A pdb=" N LYS N 40 " --> pdb=" O ARG N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 51 No H-bonds generated for 'chain 'N' and resid 49 through 51' Processing helix chain 'N' and resid 55 through 58 No H-bonds generated for 'chain 'N' and resid 55 through 58' Processing helix chain 'N' and resid 83 through 89 removed outlier: 3.714A pdb=" N LEU N 88 " --> pdb=" O VAL N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 122 removed outlier: 3.634A pdb=" N LEU N 116 " --> pdb=" O GLU N 112 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 146 No H-bonds generated for 'chain 'N' and resid 143 through 146' Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'P' and resid 7 through 26 Proline residue: P 16 - end of helix Processing helix chain 'Q' and resid 18 through 41 Processing helix chain 'V' and resid 45 through 50 Processing helix chain 'V' and resid 52 through 58 Processing helix chain 'V' and resid 126 through 139 Processing helix chain '1' and resid 26 through 33 Processing helix chain '1' and resid 68 through 71 No H-bonds generated for 'chain '1' and resid 68 through 71' Processing helix chain '1' and resid 78 through 80 No H-bonds generated for 'chain '1' and resid 78 through 80' Processing helix chain '1' and resid 95 through 97 No H-bonds generated for 'chain '1' and resid 95 through 97' Processing sheet with id= A, first strand: chain 'F' and resid 69 through 76 removed outlier: 6.809A pdb=" N ILE F 83 " --> pdb=" O TRP F 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 27 through 30 Processing sheet with id= C, first strand: chain 'H' and resid 327 through 331 Processing sheet with id= D, first strand: chain 'I' and resid 56 through 58 Processing sheet with id= E, first strand: chain 'J' and resid 37 through 41 Processing sheet with id= F, first strand: chain 'J' and resid 60 through 62 Processing sheet with id= G, first strand: chain 'K' and resid 83 through 86 removed outlier: 6.684A pdb=" N TYR K 110 " --> pdb=" O ILE K 84 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR K 86 " --> pdb=" O TYR K 110 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE K 112 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL K 143 " --> pdb=" O ALA K 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'M' and resid 15 through 17 Processing sheet with id= I, first strand: chain 'N' and resid 19 through 22 Processing sheet with id= J, first strand: chain 'N' and resid 43 through 47 Processing sheet with id= K, first strand: chain 'O' and resid 9 through 11 Processing sheet with id= L, first strand: chain 'O' and resid 59 through 62 removed outlier: 6.098A pdb=" N LYS O 51 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL O 40 " --> pdb=" O LYS O 51 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 95 through 97 removed outlier: 6.673A pdb=" N ALA S 76 " --> pdb=" O GLN S 68 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE S 70 " --> pdb=" O LYS S 74 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '1' and resid 16 through 20 removed outlier: 3.805A pdb=" N THR 1 16 " --> pdb=" O LEU 1 8 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS 1 87 " --> pdb=" O THR 1 7 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL 1 9 " --> pdb=" O CYS 1 87 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE 1 89 " --> pdb=" O VAL 1 9 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU 1 55 " --> pdb=" O LYS 1 88 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU 1 90 " --> pdb=" O LEU 1 53 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU 1 53 " --> pdb=" O LEU 1 90 " (cutoff:3.500A) 1413 hydrogen bonds defined for protein. 4002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.18 Time building geometry restraints manager: 14.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 13448 1.40 - 1.63: 19646 1.63 - 1.85: 315 1.85 - 2.07: 0 2.07 - 2.29: 40 Bond restraints: 33449 Sorted by residual: bond pdb=" C6 SQD L 101 " pdb=" S SQD L 101 " ideal model delta sigma weight residual 1.840 1.616 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C6 SQD D 601 " pdb=" S SQD D 601 " ideal model delta sigma weight residual 1.840 1.618 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C6 SQD C 201 " pdb=" S SQD C 201 " ideal model delta sigma weight residual 1.840 1.621 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C25 BCR D 602 " pdb=" C26 BCR D 602 " ideal model delta sigma weight residual 1.347 1.557 -0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C25 BCR D 603 " pdb=" C26 BCR D 603 " ideal model delta sigma weight residual 1.347 1.554 -0.207 2.00e-02 2.50e+03 1.08e+02 ... (remaining 33444 not shown) Histogram of bond angle deviations from ideal: 72.07 - 86.10: 42 86.10 - 100.14: 30 100.14 - 114.17: 20405 114.17 - 128.21: 24653 128.21 - 142.25: 330 Bond angle restraints: 45460 Sorted by residual: angle pdb=" C6 SQD C 201 " pdb=" S SQD C 201 " pdb=" O7 SQD C 201 " ideal model delta sigma weight residual 111.32 73.52 37.80 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C6 SQD D 601 " pdb=" S SQD D 601 " pdb=" O7 SQD D 601 " ideal model delta sigma weight residual 111.32 73.66 37.66 3.00e+00 1.11e-01 1.58e+02 angle pdb=" S1 FES 1 101 " pdb="FE2 FES 1 101 " pdb=" S2 FES 1 101 " ideal model delta sigma weight residual 104.33 90.06 14.27 1.14e+00 7.69e-01 1.57e+02 angle pdb=" C6 SQD L 101 " pdb=" S SQD L 101 " pdb=" O7 SQD L 101 " ideal model delta sigma weight residual 111.32 73.99 37.33 3.00e+00 1.11e-01 1.55e+02 angle pdb=" S1 FES 1 101 " pdb="FE1 FES 1 101 " pdb=" S2 FES 1 101 " ideal model delta sigma weight residual 104.33 90.10 14.23 1.20e+00 6.94e-01 1.41e+02 ... (remaining 45455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 18246 24.77 - 49.53: 1122 49.53 - 74.30: 134 74.30 - 99.06: 21 99.06 - 123.83: 8 Dihedral angle restraints: 19531 sinusoidal: 7748 harmonic: 11783 Sorted by residual: dihedral pdb=" CA TYR H 72 " pdb=" C TYR H 72 " pdb=" N ALA H 73 " pdb=" CA ALA H 73 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASP H 71 " pdb=" C ASP H 71 " pdb=" N TYR H 72 " pdb=" CA TYR H 72 " ideal model delta harmonic sigma weight residual -180.00 -152.29 -27.71 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA PRO I 164 " pdb=" C PRO I 164 " pdb=" N ALA I 165 " pdb=" CA ALA I 165 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 19528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.933: 5208 0.933 - 1.867: 0 1.867 - 2.800: 0 2.800 - 3.734: 0 3.734 - 4.667: 1 Chirality restraints: 5209 Sorted by residual: chirality pdb=" C1 SQD D 601 " pdb=" C2 SQD D 601 " pdb=" O5 SQD D 601 " pdb=" O6 SQD D 601 " both_signs ideal model delta sigma weight residual False -2.39 2.28 -4.67 2.00e-01 2.50e+01 5.45e+02 chirality pdb="FE1 SF4 K 301 " pdb=" S2 SF4 K 301 " pdb=" S3 SF4 K 301 " pdb=" S4 SF4 K 301 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" CB ILE H 154 " pdb=" CA ILE H 154 " pdb=" CG1 ILE H 154 " pdb=" CG2 ILE H 154 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.34e+00 ... (remaining 5206 not shown) Planarity restraints: 5614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 BCR D 603 " -0.279 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C17 BCR D 603 " 0.558 2.00e-02 2.50e+03 pdb=" C18 BCR D 603 " -0.290 2.00e-02 2.50e+03 pdb=" C19 BCR D 603 " -0.028 2.00e-02 2.50e+03 pdb=" C36 BCR D 603 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR D 602 " 0.491 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C11 BCR D 602 " -0.243 2.00e-02 2.50e+03 pdb=" C34 BCR D 602 " 0.110 2.00e-02 2.50e+03 pdb=" C8 BCR D 602 " -0.047 2.00e-02 2.50e+03 pdb=" C9 BCR D 602 " -0.311 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 BCR D 602 " -0.135 2.00e-02 2.50e+03 2.61e-01 8.52e+02 pdb=" C13 BCR D 602 " 0.327 2.00e-02 2.50e+03 pdb=" C14 BCR D 602 " -0.419 2.00e-02 2.50e+03 pdb=" C15 BCR D 602 " 0.199 2.00e-02 2.50e+03 pdb=" C35 BCR D 602 " 0.028 2.00e-02 2.50e+03 ... (remaining 5611 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8008 2.79 - 3.31: 30089 3.31 - 3.84: 58724 3.84 - 4.37: 70745 4.37 - 4.90: 119169 Nonbonded interactions: 286735 Sorted by model distance: nonbonded pdb=" OH TYR C 75 " pdb=" O ALA E 75 " model vdw 2.257 2.440 nonbonded pdb=" O ALA B 39 " pdb=" OG1 THR B 43 " model vdw 2.276 2.440 nonbonded pdb=" O ALA D 322 " pdb=" OH TYR D 411 " model vdw 2.287 2.440 nonbonded pdb=" OD1 ASP H 359 " pdb=" OG SER H 391 " model vdw 2.287 2.440 nonbonded pdb=" OE1 GLN B 310 " pdb=" OH TYR B 332 " model vdw 2.290 2.440 ... (remaining 286730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.460 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: 16.820 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 89.180 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.008 0.224 33449 Z= 0.547 Angle : 1.251 37.802 45460 Z= 0.573 Chirality : 0.087 4.667 5209 Planarity : 0.012 0.309 5614 Dihedral : 15.945 123.826 11995 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.94 % Favored : 91.03 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.35 (0.10), residues: 4049 helix: -2.51 (0.08), residues: 2285 sheet: -2.96 (0.34), residues: 168 loop : -3.28 (0.13), residues: 1596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 592 time to evaluate : 3.692 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 600 average time/residue: 1.4659 time to fit residues: 1043.3150 Evaluate side-chains 394 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 390 time to evaluate : 3.508 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.3128 time to fit residues: 5.1700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 4.9990 chunk 304 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 315 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 234 optimal weight: 0.5980 chunk 365 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 GLN A 339 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 HIS B 296 GLN B 340 ASN B 404 GLN ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS E 2 GLN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 HIS F 349 HIS F 570 GLN G 62 GLN G 71 ASN H 48 HIS H 205 GLN K 80 GLN K 181 HIS L 70 GLN M 9 HIS M 37 ASN N 90 ASN S 64 GLN V 49 ASN V 86 GLN 1 70 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 33449 Z= 0.179 Angle : 0.636 8.878 45460 Z= 0.313 Chirality : 0.042 0.176 5209 Planarity : 0.005 0.072 5614 Dihedral : 9.903 107.468 4789 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.62 (0.12), residues: 4049 helix: -0.87 (0.10), residues: 2288 sheet: -2.65 (0.35), residues: 177 loop : -2.89 (0.14), residues: 1584 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 443 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 32 residues processed: 491 average time/residue: 1.2678 time to fit residues: 755.8436 Evaluate side-chains 429 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 397 time to evaluate : 3.462 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 20 residues processed: 13 average time/residue: 0.7678 time to fit residues: 17.9599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 202 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 303 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 365 optimal weight: 0.3980 chunk 395 optimal weight: 0.4980 chunk 325 optimal weight: 0.0170 chunk 362 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 447 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN J 165 GLN K 80 GLN S 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 33449 Z= 0.161 Angle : 0.598 8.129 45460 Z= 0.295 Chirality : 0.041 0.162 5209 Planarity : 0.005 0.067 5614 Dihedral : 9.129 106.697 4789 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.74 (0.13), residues: 4049 helix: -0.10 (0.11), residues: 2285 sheet: -2.51 (0.36), residues: 179 loop : -2.56 (0.15), residues: 1585 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 428 time to evaluate : 3.561 Fit side-chains revert: symmetry clash outliers start: 111 outliers final: 47 residues processed: 496 average time/residue: 1.2478 time to fit residues: 755.4899 Evaluate side-chains 437 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 390 time to evaluate : 3.499 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 30 residues processed: 18 average time/residue: 0.3360 time to fit residues: 15.3252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 0.9990 chunk 274 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 174 optimal weight: 7.9990 chunk 245 optimal weight: 0.5980 chunk 367 optimal weight: 0.4980 chunk 388 optimal weight: 5.9990 chunk 191 optimal weight: 0.8980 chunk 347 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN A 212 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS I 57 HIS S 64 GLN V 135 GLN V 140 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 33449 Z= 0.187 Angle : 0.609 18.107 45460 Z= 0.297 Chirality : 0.041 0.194 5209 Planarity : 0.004 0.065 5614 Dihedral : 8.621 106.441 4789 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.13), residues: 4049 helix: 0.27 (0.11), residues: 2289 sheet: -2.57 (0.35), residues: 184 loop : -2.39 (0.15), residues: 1576 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 416 time to evaluate : 3.833 Fit side-chains outliers start: 120 outliers final: 53 residues processed: 500 average time/residue: 1.2682 time to fit residues: 776.2130 Evaluate side-chains 439 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 386 time to evaluate : 3.662 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 40 residues processed: 15 average time/residue: 0.4771 time to fit residues: 15.9672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 323 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 289 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 chunk 331 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 348 optimal weight: 0.3980 chunk 98 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN S 64 GLN V 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 33449 Z= 0.186 Angle : 0.602 15.126 45460 Z= 0.295 Chirality : 0.042 0.164 5209 Planarity : 0.004 0.066 5614 Dihedral : 8.412 106.870 4789 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer Outliers : 3.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.06 (0.13), residues: 4049 helix: 0.47 (0.11), residues: 2280 sheet: -2.51 (0.35), residues: 189 loop : -2.25 (0.15), residues: 1580 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 400 time to evaluate : 3.740 Fit side-chains outliers start: 122 outliers final: 64 residues processed: 485 average time/residue: 1.2685 time to fit residues: 751.3723 Evaluate side-chains 446 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 382 time to evaluate : 3.599 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 47 residues processed: 18 average time/residue: 0.5255 time to fit residues: 18.8904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 130 optimal weight: 0.8980 chunk 349 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 388 optimal weight: 4.9990 chunk 322 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 204 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 170 HIS S 64 GLN V 140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 33449 Z= 0.204 Angle : 0.612 15.291 45460 Z= 0.300 Chirality : 0.042 0.226 5209 Planarity : 0.004 0.065 5614 Dihedral : 8.327 107.663 4789 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.14), residues: 4049 helix: 0.62 (0.11), residues: 2273 sheet: -2.41 (0.34), residues: 195 loop : -2.16 (0.15), residues: 1581 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 395 time to evaluate : 3.981 Fit side-chains outliers start: 117 outliers final: 66 residues processed: 474 average time/residue: 1.2273 time to fit residues: 716.2502 Evaluate side-chains 439 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 373 time to evaluate : 4.078 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 47 residues processed: 20 average time/residue: 0.5841 time to fit residues: 22.5908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 374 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 221 optimal weight: 0.9980 chunk 284 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 327 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 387 optimal weight: 0.8980 chunk 242 optimal weight: 0.1980 chunk 236 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN S 64 GLN V 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 33449 Z= 0.195 Angle : 0.609 15.884 45460 Z= 0.300 Chirality : 0.042 0.221 5209 Planarity : 0.004 0.065 5614 Dihedral : 8.225 107.596 4789 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.14), residues: 4049 helix: 0.71 (0.11), residues: 2276 sheet: -2.25 (0.35), residues: 186 loop : -2.13 (0.15), residues: 1587 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 381 time to evaluate : 4.011 Fit side-chains outliers start: 103 outliers final: 59 residues processed: 458 average time/residue: 1.2450 time to fit residues: 709.5200 Evaluate side-chains 425 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 366 time to evaluate : 3.715 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 47 residues processed: 13 average time/residue: 0.6297 time to fit residues: 16.8464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 239 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 246 optimal weight: 0.6980 chunk 263 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 304 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 HIS ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN S 64 GLN V 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 33449 Z= 0.205 Angle : 0.620 15.579 45460 Z= 0.304 Chirality : 0.042 0.217 5209 Planarity : 0.004 0.064 5614 Dihedral : 8.163 107.862 4789 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.70 (0.14), residues: 4049 helix: 0.77 (0.11), residues: 2273 sheet: -2.29 (0.35), residues: 196 loop : -2.08 (0.16), residues: 1580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 382 time to evaluate : 3.474 Fit side-chains outliers start: 100 outliers final: 65 residues processed: 451 average time/residue: 1.2445 time to fit residues: 689.1674 Evaluate side-chains 431 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 366 time to evaluate : 3.636 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 50 residues processed: 17 average time/residue: 0.5135 time to fit residues: 18.2525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 0.7980 chunk 371 optimal weight: 0.6980 chunk 338 optimal weight: 6.9990 chunk 361 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 326 optimal weight: 0.8980 chunk 341 optimal weight: 5.9990 chunk 359 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 563 GLN K 80 GLN M 59 ASN S 64 GLN V 140 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 33449 Z= 0.200 Angle : 0.619 14.716 45460 Z= 0.304 Chirality : 0.042 0.208 5209 Planarity : 0.004 0.065 5614 Dihedral : 8.093 107.805 4789 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.14), residues: 4049 helix: 0.87 (0.11), residues: 2253 sheet: -2.23 (0.35), residues: 190 loop : -1.98 (0.16), residues: 1606 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 389 time to evaluate : 3.608 Fit side-chains outliers start: 84 outliers final: 57 residues processed: 455 average time/residue: 1.2716 time to fit residues: 712.5120 Evaluate side-chains 428 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 371 time to evaluate : 3.645 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 49 residues processed: 9 average time/residue: 0.4929 time to fit residues: 11.7246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 237 optimal weight: 3.9990 chunk 381 optimal weight: 0.9980 chunk 233 optimal weight: 0.4980 chunk 181 optimal weight: 2.9990 chunk 265 optimal weight: 0.9990 chunk 400 optimal weight: 9.9990 chunk 368 optimal weight: 5.9990 chunk 318 optimal weight: 0.3980 chunk 33 optimal weight: 0.4980 chunk 246 optimal weight: 0.4980 chunk 195 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN N 87 HIS S 64 GLN V 49 ASN V 140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 33449 Z= 0.182 Angle : 0.625 17.008 45460 Z= 0.306 Chirality : 0.042 0.207 5209 Planarity : 0.004 0.062 5614 Dihedral : 7.995 107.380 4789 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.14), residues: 4049 helix: 0.95 (0.11), residues: 2244 sheet: -2.32 (0.37), residues: 167 loop : -1.96 (0.15), residues: 1638 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 391 time to evaluate : 3.621 Fit side-chains outliers start: 72 outliers final: 56 residues processed: 451 average time/residue: 1.2859 time to fit residues: 712.3321 Evaluate side-chains 426 residues out of total 3372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 370 time to evaluate : 3.971 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 50 residues processed: 8 average time/residue: 0.3780 time to fit residues: 10.4504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 253 optimal weight: 0.7980 chunk 339 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 319 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 327 optimal weight: 0.0570 chunk 40 optimal weight: 0.3980 chunk 58 optimal weight: 0.0970 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.101894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.086038 restraints weight = 72215.142| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.00 r_work: 0.3313 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 33449 Z= 0.174 Angle : 0.622 15.868 45460 Z= 0.304 Chirality : 0.041 0.201 5209 Planarity : 0.004 0.067 5614 Dihedral : 7.881 107.283 4789 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.14), residues: 4049 helix: 1.04 (0.11), residues: 2240 sheet: -2.32 (0.37), residues: 165 loop : -1.94 (0.15), residues: 1644 =============================================================================== Job complete usr+sys time: 12005.08 seconds wall clock time: 214 minutes 14.07 seconds (12854.07 seconds total)