Starting phenix.real_space_refine on Mon Nov 20 06:04:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbw_21146/11_2023/6vbw_21146_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbw_21146/11_2023/6vbw_21146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbw_21146/11_2023/6vbw_21146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbw_21146/11_2023/6vbw_21146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbw_21146/11_2023/6vbw_21146_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbw_21146/11_2023/6vbw_21146_neut.pdb" } resolution = 3.2 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 4 6.06 5 P 106 5.49 5 S 151 5.16 5 C 18147 2.51 5 N 5035 2.21 5 O 5644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ASP 608": "OD1" <-> "OD2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 291": "NH1" <-> "NH2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D ARG 286": "NH1" <-> "NH2" Residue "D PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "F PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F ARG 286": "NH1" <-> "NH2" Residue "F PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 291": "NH1" <-> "NH2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E ARG 286": "NH1" <-> "NH2" Residue "E PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 291": "NH1" <-> "NH2" Residue "G PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 98": "NH1" <-> "NH2" Residue "G PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G GLU 277": "OE1" <-> "OE2" Residue "G ARG 286": "NH1" <-> "NH2" Residue "G PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 291": "NH1" <-> "NH2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H ARG 102": "NH1" <-> "NH2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I ARG 20": "NH1" <-> "NH2" Residue "I ARG 58": "NH1" <-> "NH2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 220": "NH1" <-> "NH2" Residue "I ARG 274": "NH1" <-> "NH2" Residue "J ARG 5": "NH1" <-> "NH2" Residue "J ARG 20": "NH1" <-> "NH2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 71": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 117": "NH1" <-> "NH2" Residue "J ARG 220": "NH1" <-> "NH2" Residue "J ARG 274": "NH1" <-> "NH2" Residue "J TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 29087 Number of models: 1 Model: "" Number of chains: 15 Chain: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 807 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "K" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1275 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 16, 'rna3p_pur': 20, 'rna3p_pyr': 15} Link IDs: {'rna2p': 25, 'rna3p': 35} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3538 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 8 Chain: "B" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2704 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2713 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 17, 'TRANS': 321} Chain breaks: 1 Chain: "D" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2729 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 17, 'TRANS': 323} Chain breaks: 1 Chain: "F" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2729 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 17, 'TRANS': 323} Chain breaks: 1 Chain: "E" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2720 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain breaks: 1 Chain: "G" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2490 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 15, 'TRANS': 291} Chain breaks: 2 Chain: "H" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1113 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 4 Chain: "I" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3050 Classifications: {'peptide': 374} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 355} Chain breaks: 3 Chain: "J" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3075 Classifications: {'peptide': 378} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 359} Chain breaks: 2 Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23981 SG CYS I 128 72.997 57.935 19.198 1.00 80.43 S ATOM 24002 SG CYS I 131 68.813 57.124 20.895 1.00 80.78 S ATOM 24256 SG CYS I 161 79.685 69.141 13.876 1.00 82.72 S ATOM 24405 SG CYS I 181 78.026 71.966 11.567 1.00 82.94 S ATOM 27052 SG CYS J 131 47.969 21.496 60.377 1.00 92.95 S Time building chain proxies: 15.37, per 1000 atoms: 0.53 Number of scatterers: 29087 At special positions: 0 Unit cell: (122.36, 201.096, 186.2, 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 4 29.99 S 151 16.00 P 106 15.00 O 5644 8.00 N 5035 7.00 C 18147 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: 11.48 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 401 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 131 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 128 " pdb="ZN ZN I 401 " - pdb=" ND1 HIS I 153 " pdb=" ZN I 402 " pdb="ZN ZN I 402 " - pdb=" SG CYS I 161 " pdb="ZN ZN I 402 " - pdb=" SG CYS I 181 " pdb=" ZN J 401 " pdb="ZN ZN J 401 " - pdb=" SG CYS J 131 " 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6370 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 51 sheets defined 33.0% alpha, 13.9% beta 16 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 9.94 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 3.728A pdb=" N PHE A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.750A pdb=" N ILE A 76 " --> pdb=" O TRP A 72 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 79 " --> pdb=" O CYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.611A pdb=" N TYR A 129 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 130 " --> pdb=" O SER A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 130' Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.700A pdb=" N LYS A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.602A pdb=" N HIS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.579A pdb=" N PHE A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 499 removed outlier: 3.966A pdb=" N LEU A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 519 removed outlier: 4.368A pdb=" N LYS A 517 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 519 " --> pdb=" O PHE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.622A pdb=" N GLU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.842A pdb=" N ALA A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 105 through 123 removed outlier: 3.697A pdb=" N THR B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.534A pdb=" N ALA B 129 " --> pdb=" O TRP B 125 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 136 " --> pdb=" O TYR B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 3.577A pdb=" N LEU B 142 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LYS B 144 " --> pdb=" O TRP B 141 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 146 " --> pdb=" O TRP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.807A pdb=" N PHE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 removed outlier: 3.816A pdb=" N THR B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 removed outlier: 3.892A pdb=" N GLY B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.643A pdb=" N GLN B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 319 removed outlier: 3.760A pdb=" N GLU B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 344 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.730A pdb=" N ALA C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 removed outlier: 3.546A pdb=" N GLN C 114 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 4.184A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.777A pdb=" N PHE C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 200 Processing helix chain 'C' and resid 260 through 269 removed outlier: 3.558A pdb=" N ALA C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.506A pdb=" N ILE C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 314 through 321 removed outlier: 3.615A pdb=" N GLU C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 344 removed outlier: 4.286A pdb=" N MET C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'D' and resid 105 through 123 removed outlier: 4.145A pdb=" N VAL D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 4.103A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 136 " --> pdb=" O TYR D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 175 Processing helix chain 'D' and resid 177 through 183 removed outlier: 3.607A pdb=" N PHE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 197 removed outlier: 3.679A pdb=" N ILE D 194 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 removed outlier: 3.757A pdb=" N ALA D 267 " --> pdb=" O LYS D 263 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 314 through 322 removed outlier: 3.744A pdb=" N GLU D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 342 removed outlier: 3.654A pdb=" N PHE D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 123 removed outlier: 3.508A pdb=" N LYS F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN F 114 " --> pdb=" O GLN F 110 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR F 121 " --> pdb=" O GLU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 135 removed outlier: 3.501A pdb=" N ALA F 129 " --> pdb=" O TRP F 125 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 183 Processing helix chain 'F' and resid 184 through 186 No H-bonds generated for 'chain 'F' and resid 184 through 186' Processing helix chain 'F' and resid 187 through 198 removed outlier: 3.754A pdb=" N GLU F 192 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 269 removed outlier: 3.821A pdb=" N ALA F 267 " --> pdb=" O LYS F 263 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 269 " --> pdb=" O GLY F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 311 removed outlier: 3.518A pdb=" N GLN F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 321 removed outlier: 4.248A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F 319 " --> pdb=" O HIS F 315 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU F 320 " --> pdb=" O TYR F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 340 removed outlier: 4.245A pdb=" N ASP F 333 " --> pdb=" O GLU F 329 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET F 334 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN F 340 " --> pdb=" O PHE F 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 99 removed outlier: 3.576A pdb=" N ARG E 98 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN E 99 " --> pdb=" O GLU E 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 95 through 99' Processing helix chain 'E' and resid 105 through 113 removed outlier: 3.639A pdb=" N GLN E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 123 removed outlier: 3.911A pdb=" N THR E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 138 removed outlier: 4.003A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE E 136 " --> pdb=" O TYR E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 175 Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 187 through 200 removed outlier: 3.803A pdb=" N MET E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE E 194 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 269 removed outlier: 3.822A pdb=" N ALA E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA E 269 " --> pdb=" O GLY E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 312 through 321 removed outlier: 3.547A pdb=" N ILE E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 330 Processing helix chain 'E' and resid 331 through 344 removed outlier: 3.516A pdb=" N ASN E 340 " --> pdb=" O PHE E 336 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E 341 " --> pdb=" O LEU E 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 123 removed outlier: 3.646A pdb=" N GLN G 114 " --> pdb=" O GLN G 110 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 138 removed outlier: 3.746A pdb=" N ASN G 135 " --> pdb=" O ARG G 131 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G 136 " --> pdb=" O TYR G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 175 Processing helix chain 'G' and resid 177 through 183 removed outlier: 3.946A pdb=" N PHE G 181 " --> pdb=" O SER G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 200 removed outlier: 4.205A pdb=" N MET G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE G 194 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR G 196 " --> pdb=" O GLU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 269 removed outlier: 3.945A pdb=" N ALA G 267 " --> pdb=" O LYS G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 311 Processing helix chain 'G' and resid 314 through 321 removed outlier: 3.806A pdb=" N GLU G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL G 319 " --> pdb=" O HIS G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 340 removed outlier: 3.640A pdb=" N ASP G 333 " --> pdb=" O GLU G 329 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET G 334 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN G 340 " --> pdb=" O PHE G 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 35 removed outlier: 3.928A pdb=" N LYS H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS H 24 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG H 26 " --> pdb=" O ALA H 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN H 32 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR H 33 " --> pdb=" O HIS H 29 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN H 34 " --> pdb=" O GLY H 30 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 80 removed outlier: 4.264A pdb=" N GLN H 76 " --> pdb=" O HIS H 72 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 123 Processing helix chain 'I' and resid 13 through 25 removed outlier: 3.721A pdb=" N ILE I 19 " --> pdb=" O GLU I 15 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA I 22 " --> pdb=" O PHE I 18 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 3.877A pdb=" N PHE I 33 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 60 removed outlier: 3.654A pdb=" N ILE I 59 " --> pdb=" O ILE I 56 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASN I 60 " --> pdb=" O THR I 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 56 through 60' Processing helix chain 'I' and resid 67 through 82 removed outlier: 4.029A pdb=" N LYS I 77 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU I 78 " --> pdb=" O SER I 74 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA I 79 " --> pdb=" O PHE I 75 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLN I 80 " --> pdb=" O LEU I 76 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 120 No H-bonds generated for 'chain 'I' and resid 118 through 120' Processing helix chain 'I' and resid 139 through 144 Processing helix chain 'I' and resid 197 through 206 removed outlier: 3.712A pdb=" N GLY I 206 " --> pdb=" O ASN I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 232 removed outlier: 3.755A pdb=" N TRP I 226 " --> pdb=" O GLY I 222 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET I 228 " --> pdb=" O VAL I 224 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY I 229 " --> pdb=" O HIS I 225 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE I 230 " --> pdb=" O TRP I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 245 removed outlier: 3.559A pdb=" N VAL I 241 " --> pdb=" O HIS I 237 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE I 244 " --> pdb=" O PHE I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 264 removed outlier: 3.842A pdb=" N ILE I 254 " --> pdb=" O SER I 250 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE I 255 " --> pdb=" O PHE I 251 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU I 260 " --> pdb=" O GLU I 256 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU I 264 " --> pdb=" O GLU I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 279 Processing helix chain 'I' and resid 279 through 285 Processing helix chain 'I' and resid 297 through 309 removed outlier: 3.849A pdb=" N GLY I 301 " --> pdb=" O ASN I 297 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN I 309 " --> pdb=" O CYS I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 320 Processing helix chain 'I' and resid 325 through 333 removed outlier: 3.529A pdb=" N THR I 329 " --> pdb=" O ALA I 325 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET I 331 " --> pdb=" O GLU I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 345 removed outlier: 3.638A pdb=" N ILE I 339 " --> pdb=" O SER I 335 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU I 344 " --> pdb=" O ALA I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 380 removed outlier: 4.495A pdb=" N CYS I 374 " --> pdb=" O GLY I 370 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU I 375 " --> pdb=" O ASP I 371 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA I 378 " --> pdb=" O CYS I 374 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE I 380 " --> pdb=" O TRP I 376 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 25 removed outlier: 3.667A pdb=" N PHE J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE J 19 " --> pdb=" O GLU J 15 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG J 20 " --> pdb=" O SER J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 44 removed outlier: 3.565A pdb=" N ASP J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE J 44 " --> pdb=" O PHE J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 52 removed outlier: 3.519A pdb=" N PHE J 52 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 removed outlier: 3.768A pdb=" N ILE J 59 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN J 60 " --> pdb=" O THR J 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 60' Processing helix chain 'J' and resid 67 through 82 removed outlier: 3.642A pdb=" N THR J 72 " --> pdb=" O SER J 68 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA J 73 " --> pdb=" O SER J 69 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA J 79 " --> pdb=" O PHE J 75 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 93 removed outlier: 3.665A pdb=" N ALA J 93 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 135 Processing helix chain 'J' and resid 139 through 144 removed outlier: 3.648A pdb=" N TRP J 142 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS J 143 " --> pdb=" O TYR J 140 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE J 144 " --> pdb=" O LEU J 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 139 through 144' Processing helix chain 'J' and resid 197 through 204 Processing helix chain 'J' and resid 216 through 232 removed outlier: 3.811A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU J 223 " --> pdb=" O TYR J 219 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL J 224 " --> pdb=" O ARG J 220 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS J 225 " --> pdb=" O TRP J 221 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP J 226 " --> pdb=" O GLY J 222 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY J 229 " --> pdb=" O HIS J 225 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS J 231 " --> pdb=" O TRP J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 244 removed outlier: 3.696A pdb=" N PHE J 244 " --> pdb=" O PHE J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 265 removed outlier: 3.573A pdb=" N GLU J 256 " --> pdb=" O HIS J 252 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU J 264 " --> pdb=" O GLU J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 280 Processing helix chain 'J' and resid 282 through 286 removed outlier: 3.913A pdb=" N SER J 286 " --> pdb=" O PHE J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 309 removed outlier: 4.060A pdb=" N CYS J 305 " --> pdb=" O GLY J 301 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU J 307 " --> pdb=" O LEU J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 320 Processing helix chain 'J' and resid 325 through 333 removed outlier: 3.755A pdb=" N THR J 329 " --> pdb=" O ALA J 325 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL J 330 " --> pdb=" O LEU J 326 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET J 331 " --> pdb=" O GLU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 345 removed outlier: 3.548A pdb=" N ILE J 339 " --> pdb=" O SER J 335 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU J 344 " --> pdb=" O ALA J 340 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN J 345 " --> pdb=" O SER J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 380 removed outlier: 3.589A pdb=" N LEU J 377 " --> pdb=" O PHE J 373 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA J 378 " --> pdb=" O CYS J 374 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.718A pdb=" N ALA A 217 " --> pdb=" O ASN A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 201 through 204 removed outlier: 4.316A pdb=" N LYS A 587 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 569 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLY A 596 " --> pdb=" O CYS A 567 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N CYS A 567 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 598 " --> pdb=" O ALA A 565 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 16.150A pdb=" N SER A 566 " --> pdb=" O PRO A 627 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 568 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA6, first strand: chain 'A' and resid 503 through 504 removed outlier: 5.854A pdb=" N PHE A 479 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 447 through 450 removed outlier: 4.391A pdb=" N ASP A 472 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.728A pdb=" N TYR B 9 " --> pdb=" O GLY B 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 41 removed outlier: 3.536A pdb=" N VAL B 73 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 88 through 89 removed outlier: 3.844A pdb=" N CYS B 151 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP B 152 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B 170 " --> pdb=" O TRP B 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AB4, first strand: chain 'B' and resid 270 through 272 Processing sheet with id=AB5, first strand: chain 'B' and resid 289 through 290 removed outlier: 3.740A pdb=" N THR B 295 " --> pdb=" O HIS B 290 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 102 through 103 removed outlier: 3.963A pdb=" N GLY C 345 " --> pdb=" O TYR C 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.511A pdb=" N CYS C 19 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 88 " --> pdb=" O CYS C 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS C 84 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP C 152 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 170 " --> pdb=" O TRP C 152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 29 through 31 removed outlier: 4.201A pdb=" N PHE C 20 " --> pdb=" O PRO C 257 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N VAL C 22 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ARG C 255 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 35 through 41 Processing sheet with id=AC1, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.692A pdb=" N THR C 295 " --> pdb=" O HIS C 290 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 102 through 103 removed outlier: 3.759A pdb=" N GLY D 345 " --> pdb=" O TYR D 9 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.616A pdb=" N CYS D 87 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 29 through 31 removed outlier: 4.093A pdb=" N PHE D 20 " --> pdb=" O PRO D 257 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N VAL D 22 " --> pdb=" O ARG D 255 " (cutoff:3.500A) removed outlier: 14.201A pdb=" N ARG D 255 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 35 through 41 Processing sheet with id=AC6, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AC7, first strand: chain 'D' and resid 289 through 290 removed outlier: 3.693A pdb=" N THR D 295 " --> pdb=" O HIS D 290 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 102 through 103 removed outlier: 3.659A pdb=" N GLY F 345 " --> pdb=" O TYR F 9 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 29 through 31 removed outlier: 3.606A pdb=" N CYS F 19 " --> pdb=" O SER F 88 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER F 88 " --> pdb=" O CYS F 19 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS F 87 " --> pdb=" O ALA F 211 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N CYS F 151 " --> pdb=" O HIS F 214 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP F 152 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP F 170 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL F 166 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 29 through 31 removed outlier: 4.075A pdb=" N PHE F 20 " --> pdb=" O PRO F 257 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N VAL F 22 " --> pdb=" O ARG F 255 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N ARG F 255 " --> pdb=" O VAL F 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 35 through 41 removed outlier: 3.515A pdb=" N VAL F 73 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN F 69 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AD4, first strand: chain 'F' and resid 289 through 290 removed outlier: 3.843A pdb=" N THR F 295 " --> pdb=" O HIS F 290 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AD6, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.516A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 24 current: chain 'E' and resid 151 through 156 Processing sheet with id=AD7, first strand: chain 'E' and resid 28 through 31 removed outlier: 3.566A pdb=" N ARG E 28 " --> pdb=" O TRP E 24 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 84 through 93 current: chain 'E' and resid 248 through 250 Processing sheet with id=AD8, first strand: chain 'E' and resid 35 through 41 removed outlier: 3.772A pdb=" N ASN E 35 " --> pdb=" O PHE E 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 270 through 272 Processing sheet with id=AE1, first strand: chain 'E' and resid 289 through 290 removed outlier: 3.508A pdb=" N THR E 295 " --> pdb=" O HIS E 290 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 102 through 103 removed outlier: 3.707A pdb=" N GLY G 345 " --> pdb=" O TYR G 9 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 18 through 24 current: chain 'G' and resid 152 through 156 Processing sheet with id=AE4, first strand: chain 'G' and resid 28 through 31 removed outlier: 3.813A pdb=" N ARG G 28 " --> pdb=" O TRP G 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 84 through 93 current: chain 'G' and resid 248 through 250 Processing sheet with id=AE5, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AE6, first strand: chain 'G' and resid 270 through 272 Processing sheet with id=AE7, first strand: chain 'G' and resid 289 through 290 Processing sheet with id=AE8, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.511A pdb=" N SER H 57 " --> pdb=" O SER H 43 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 102 through 103 removed outlier: 3.789A pdb=" N ARG H 102 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG H 168 " --> pdb=" O ARG H 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'H' and resid 153 through 155 Processing sheet with id=AF2, first strand: chain 'I' and resid 95 through 97 removed outlier: 4.147A pdb=" N ALA I 107 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 149 through 150 removed outlier: 3.861A pdb=" N VAL I 155 " --> pdb=" O CYS I 150 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 322 through 323 removed outlier: 3.516A pdb=" N PHE I 367 " --> pdb=" O MET I 323 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 95 through 100 removed outlier: 4.113A pdb=" N THR J 97 " --> pdb=" O ALA J 107 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ALA J 107 " --> pdb=" O THR J 97 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 322 through 323 765 hydrogen bonds defined for protein. 2100 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 9.86 Time building geometry restraints manager: 12.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5920 1.33 - 1.45: 8095 1.45 - 1.57: 15592 1.57 - 1.69: 209 1.69 - 1.82: 219 Bond restraints: 30035 Sorted by residual: bond pdb=" N ILE C 258 " pdb=" CA ILE C 258 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.13e+01 bond pdb=" N ILE D 258 " pdb=" CA ILE D 258 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.03e+01 bond pdb=" N ILE A 211 " pdb=" CA ILE A 211 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.92e+00 bond pdb=" N ILE F 258 " pdb=" CA ILE F 258 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.08e-02 8.57e+03 9.64e+00 bond pdb=" N SER A 521 " pdb=" CA SER A 521 " ideal model delta sigma weight residual 1.453 1.491 -0.037 1.22e-02 6.72e+03 9.41e+00 ... (remaining 30030 not shown) Histogram of bond angle deviations from ideal: 93.99 - 102.32: 186 102.32 - 110.65: 10221 110.65 - 118.98: 14896 118.98 - 127.31: 15328 127.31 - 135.64: 581 Bond angle restraints: 41212 Sorted by residual: angle pdb=" CA GLY B 345 " pdb=" C GLY B 345 " pdb=" O GLY B 345 " ideal model delta sigma weight residual 122.23 118.21 4.02 6.90e-01 2.10e+00 3.39e+01 angle pdb=" O3' DA L 76 " pdb=" C3' DA L 76 " pdb=" C2' DA L 76 " ideal model delta sigma weight residual 111.50 119.94 -8.44 1.50e+00 4.44e-01 3.17e+01 angle pdb=" C LEU F 40 " pdb=" N GLY F 41 " pdb=" CA GLY F 41 " ideal model delta sigma weight residual 122.43 117.84 4.59 8.90e-01 1.26e+00 2.66e+01 angle pdb=" C4' U K 21 " pdb=" C3' U K 21 " pdb=" O3' U K 21 " ideal model delta sigma weight residual 109.40 101.95 7.45 1.50e+00 4.44e-01 2.46e+01 angle pdb=" C ALA E 45 " pdb=" N ALA E 46 " pdb=" CA ALA E 46 " ideal model delta sigma weight residual 121.54 130.98 -9.44 1.91e+00 2.74e-01 2.45e+01 ... (remaining 41207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 17125 34.55 - 69.11: 376 69.11 - 103.66: 37 103.66 - 138.21: 2 138.21 - 172.76: 2 Dihedral angle restraints: 17542 sinusoidal: 7747 harmonic: 9795 Sorted by residual: dihedral pdb=" O4' U K 42 " pdb=" C1' U K 42 " pdb=" N1 U K 42 " pdb=" C2 U K 42 " ideal model delta sinusoidal sigma weight residual 200.00 76.45 123.55 1 1.50e+01 4.44e-03 6.62e+01 dihedral pdb=" O4' U K 20 " pdb=" C1' U K 20 " pdb=" N1 U K 20 " pdb=" C2 U K 20 " ideal model delta sinusoidal sigma weight residual -128.00 44.76 -172.76 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C K 38 " pdb=" C1' C K 38 " pdb=" N1 C K 38 " pdb=" C2 C K 38 " ideal model delta sinusoidal sigma weight residual 232.00 66.31 165.69 1 1.70e+01 3.46e-03 6.54e+01 ... (remaining 17539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3653 0.081 - 0.163: 761 0.163 - 0.244: 122 0.244 - 0.325: 31 0.325 - 0.406: 2 Chirality restraints: 4569 Sorted by residual: chirality pdb=" C3' DA L 76 " pdb=" C4' DA L 76 " pdb=" O3' DA L 76 " pdb=" C2' DA L 76 " both_signs ideal model delta sigma weight residual False -2.66 -2.25 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CA ARG A 584 " pdb=" N ARG A 584 " pdb=" C ARG A 584 " pdb=" CB ARG A 584 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CG LEU C 215 " pdb=" CB LEU C 215 " pdb=" CD1 LEU C 215 " pdb=" CD2 LEU C 215 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 4566 not shown) Planarity restraints: 4876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 9 " -0.026 2.00e-02 2.50e+03 2.45e-02 1.20e+01 pdb=" CG TYR E 9 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR E 9 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR E 9 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR E 9 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR E 9 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 9 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 9 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 9 " 0.025 2.00e-02 2.50e+03 2.42e-02 1.17e+01 pdb=" CG TYR G 9 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR G 9 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR G 9 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR G 9 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR G 9 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR G 9 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR G 9 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 9 " 0.023 2.00e-02 2.50e+03 2.39e-02 1.14e+01 pdb=" CG TYR F 9 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR F 9 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR F 9 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR F 9 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR F 9 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR F 9 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR F 9 " 0.004 2.00e-02 2.50e+03 ... (remaining 4873 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 404 2.63 - 3.19: 23840 3.19 - 3.76: 44254 3.76 - 4.33: 62797 4.33 - 4.90: 103041 Nonbonded interactions: 234336 Sorted by model distance: nonbonded pdb=" O2' U K 21 " pdb=" O4' U K 22 " model vdw 2.057 2.440 nonbonded pdb=" O2' G K 18 " pdb=" O4' C K 19 " model vdw 2.088 2.440 nonbonded pdb=" O2 C K 46 " pdb=" N2 G K 60 " model vdw 2.129 2.520 nonbonded pdb=" O ASP A 183 " pdb=" OD1 ASP A 183 " model vdw 2.137 3.040 nonbonded pdb=" O SER G 95 " pdb=" OG SER G 95 " model vdw 2.138 2.440 ... (remaining 234331 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 39 or resid 71 through 229 or resid 243 through \ 349)) selection = (chain 'C' and (resid 1 through 39 or resid 71 through 229 or resid 243 through \ 349)) selection = (chain 'D' and (resid 1 through 39 or resid 71 through 229 or resid 243 through \ 349)) selection = (chain 'E' and (resid 1 through 39 or resid 71 through 229 or resid 243 through \ 349)) selection = (chain 'F' and (resid 1 through 39 or resid 71 through 229 or resid 243 through \ 349)) selection = (chain 'G' and (resid 1 through 229 or resid 243 through 349)) } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 1 through 265 or resid 270 through 391 or resid 401 throug \ h 402)) } 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: 1.190 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: 0.020 Extract box with map and model: 6.660 Check model and map are aligned: 0.470 Set scattering table: 0.250 Process input model: 84.750 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.011 0.119 30035 Z= 0.725 Angle : 1.187 14.283 41212 Z= 0.693 Chirality : 0.072 0.406 4569 Planarity : 0.008 0.072 4876 Dihedral : 14.357 172.765 11172 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.52 % Favored : 91.39 % Rotamer: Outliers : 1.96 % Allowed : 4.66 % Favored : 93.38 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.97 % 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: -4.69 (0.11), residues: 3275 helix: -4.22 (0.08), residues: 1021 sheet: -2.19 (0.22), residues: 491 loop : -2.69 (0.12), residues: 1763 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 632 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 21 residues processed: 676 average time/residue: 0.4760 time to fit residues: 486.7748 Evaluate side-chains 428 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 407 time to evaluate : 3.196 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3244 time to fit residues: 16.3758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 7.9990 chunk 257 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 137 optimal weight: 0.0980 chunk 266 optimal weight: 0.4980 chunk 103 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 308 optimal weight: 50.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS A 227 GLN A 420 HIS A 486 ASN A 493 GLN A 562 GLN A 581 ASN B 6 ASN B 72 GLN B 77 HIS B 299 HIS B 332 ASN C 77 HIS C 153 ASN C 299 HIS C 349 HIS D 77 HIS D 145 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN D 299 HIS D 349 HIS F 77 HIS F 110 GLN F 145 ASN F 214 HIS F 299 HIS F 311 GLN F 349 HIS E 77 HIS E 299 HIS E 349 HIS G 72 GLN G 179 GLN G 299 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN H 71 GLN H 105 GLN I 46 HIS I 60 ASN I 66 ASN I 151 HIS I 153 HIS I 194 HIS I 214 ASN I 237 HIS I 320 ASN J 237 HIS J 296 HIS J 309 ASN J 324 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30035 Z= 0.182 Angle : 0.616 9.390 41212 Z= 0.328 Chirality : 0.042 0.215 4569 Planarity : 0.006 0.058 4876 Dihedral : 14.684 177.761 4767 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.77 % Allowed : 9.72 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -3.49 (0.13), residues: 3275 helix: -2.72 (0.12), residues: 1061 sheet: -1.74 (0.22), residues: 517 loop : -2.19 (0.13), residues: 1697 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 448 time to evaluate : 3.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 35 residues processed: 517 average time/residue: 0.4907 time to fit residues: 394.2786 Evaluate side-chains 379 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 344 time to evaluate : 3.267 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3037 time to fit residues: 23.4036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 0.0670 chunk 95 optimal weight: 0.8980 chunk 256 optimal weight: 0.0470 chunk 210 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 309 optimal weight: 10.0000 chunk 334 optimal weight: 8.9990 chunk 275 optimal weight: 8.9990 chunk 306 optimal weight: 30.0000 chunk 105 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 overall best weight: 1.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN B 311 GLN C 42 GLN C 72 GLN C 311 GLN ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN F 145 ASN F 179 GLN E 72 GLN E 349 HIS G 214 HIS G 349 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 324 ASN J 381 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 30035 Z= 0.268 Angle : 0.619 8.422 41212 Z= 0.323 Chirality : 0.043 0.199 4569 Planarity : 0.005 0.052 4876 Dihedral : 14.461 176.163 4767 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.67 % Allowed : 11.75 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -2.83 (0.13), residues: 3275 helix: -1.85 (0.14), residues: 1052 sheet: -1.49 (0.22), residues: 530 loop : -1.99 (0.14), residues: 1693 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 365 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 42 residues processed: 429 average time/residue: 0.4515 time to fit residues: 301.0320 Evaluate side-chains 366 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 324 time to evaluate : 3.472 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2718 time to fit residues: 25.8676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 310 optimal weight: 40.0000 chunk 328 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 294 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 HIS ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 HIS B 72 GLN B 332 ASN B 348 GLN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 348 GLN D 42 GLN D 84 HIS ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN F 110 GLN F 179 GLN G 183 ASN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS I 151 HIS I 345 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 30035 Z= 0.364 Angle : 0.653 9.593 41212 Z= 0.341 Chirality : 0.045 0.259 4569 Planarity : 0.005 0.054 4876 Dihedral : 14.475 175.721 4767 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.36 % Allowed : 13.67 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -2.61 (0.14), residues: 3275 helix: -1.50 (0.14), residues: 1068 sheet: -1.56 (0.22), residues: 553 loop : -1.90 (0.14), residues: 1654 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 336 time to evaluate : 3.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 31 residues processed: 392 average time/residue: 0.4402 time to fit residues: 268.2970 Evaluate side-chains 345 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 314 time to evaluate : 3.511 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2794 time to fit residues: 20.9038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 6.9990 chunk 186 optimal weight: 0.1980 chunk 4 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 280 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 294 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN B 332 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30035 Z= 0.184 Angle : 0.543 9.334 41212 Z= 0.285 Chirality : 0.040 0.202 4569 Planarity : 0.004 0.050 4876 Dihedral : 14.239 179.112 4767 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.35 % Allowed : 15.02 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -2.22 (0.14), residues: 3275 helix: -1.03 (0.15), residues: 1075 sheet: -1.39 (0.22), residues: 552 loop : -1.75 (0.14), residues: 1648 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 338 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 12 residues processed: 367 average time/residue: 0.4704 time to fit residues: 264.9662 Evaluate side-chains 324 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 312 time to evaluate : 3.233 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2752 time to fit residues: 10.6176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 2.9990 chunk 295 optimal weight: 20.0000 chunk 64 optimal weight: 0.0370 chunk 192 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 328 optimal weight: 0.9980 chunk 273 optimal weight: 3.9990 chunk 152 optimal weight: 0.0370 chunk 27 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN B 72 GLN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN D 55 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN G 183 ASN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30035 Z= 0.236 Angle : 0.565 8.802 41212 Z= 0.294 Chirality : 0.041 0.213 4569 Planarity : 0.005 0.050 4876 Dihedral : 14.168 177.808 4767 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.76 % Allowed : 15.16 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -2.02 (0.14), residues: 3275 helix: -0.78 (0.15), residues: 1072 sheet: -1.28 (0.23), residues: 546 loop : -1.71 (0.14), residues: 1657 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 327 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 23 residues processed: 363 average time/residue: 0.4742 time to fit residues: 268.1359 Evaluate side-chains 343 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 320 time to evaluate : 3.385 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2994 time to fit residues: 17.7677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 50.0000 chunk 37 optimal weight: 5.9990 chunk 187 optimal weight: 0.5980 chunk 240 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 276 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 327 optimal weight: 0.0980 chunk 205 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN C 311 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30035 Z= 0.198 Angle : 0.539 9.107 41212 Z= 0.280 Chirality : 0.040 0.188 4569 Planarity : 0.004 0.054 4876 Dihedral : 14.093 179.061 4767 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.88 % Allowed : 16.04 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.81 (0.14), residues: 3275 helix: -0.55 (0.16), residues: 1077 sheet: -1.23 (0.23), residues: 533 loop : -1.60 (0.14), residues: 1665 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 342 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 365 average time/residue: 0.4649 time to fit residues: 261.5653 Evaluate side-chains 329 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 319 time to evaluate : 3.027 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2655 time to fit residues: 9.1584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 208 optimal weight: 0.5980 chunk 223 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 257 optimal weight: 0.0970 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN D 71 HIS ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 GLN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS I 151 HIS ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30035 Z= 0.247 Angle : 0.571 9.357 41212 Z= 0.296 Chirality : 0.042 0.186 4569 Planarity : 0.005 0.060 4876 Dihedral : 14.099 178.015 4767 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.78 % Allowed : 16.71 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.75 (0.14), residues: 3275 helix: -0.43 (0.16), residues: 1067 sheet: -1.23 (0.23), residues: 536 loop : -1.59 (0.14), residues: 1672 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 326 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 343 average time/residue: 0.4779 time to fit residues: 255.8590 Evaluate side-chains 337 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 324 time to evaluate : 3.457 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3042 time to fit residues: 11.7622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 20.0000 chunk 313 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 305 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 93 optimal weight: 0.0470 chunk 275 optimal weight: 5.9990 chunk 288 optimal weight: 0.9990 chunk 304 optimal weight: 10.0000 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN A 272 HIS ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS I 154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 30035 Z= 0.357 Angle : 0.634 10.031 41212 Z= 0.329 Chirality : 0.045 0.188 4569 Planarity : 0.005 0.066 4876 Dihedral : 14.266 176.341 4767 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.64 % Allowed : 16.95 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.87 (0.14), residues: 3275 helix: -0.52 (0.16), residues: 1070 sheet: -1.23 (0.23), residues: 550 loop : -1.71 (0.14), residues: 1655 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 325 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 338 average time/residue: 0.4639 time to fit residues: 242.9546 Evaluate side-chains 326 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 317 time to evaluate : 3.446 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2814 time to fit residues: 9.4156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 0.0060 chunk 322 optimal weight: 0.2980 chunk 197 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 338 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 208 optimal weight: 0.4980 chunk 165 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN B 72 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 30035 Z= 0.149 Angle : 0.522 9.804 41212 Z= 0.273 Chirality : 0.039 0.171 4569 Planarity : 0.004 0.065 4876 Dihedral : 14.049 179.305 4767 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.14 % Allowed : 17.56 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.49 (0.14), residues: 3275 helix: -0.09 (0.16), residues: 1062 sheet: -1.07 (0.24), residues: 531 loop : -1.54 (0.14), residues: 1682 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 345 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 349 average time/residue: 0.4756 time to fit residues: 257.7748 Evaluate side-chains 325 residues out of total 2962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 323 time to evaluate : 3.509 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2849 time to fit residues: 5.8014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 0.5980 chunk 287 optimal weight: 0.0370 chunk 82 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 270 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 277 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 311 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS I 151 HIS ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 ASN J 262 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.187863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.144902 restraints weight = 37952.169| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.39 r_work: 0.3115 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30035 Z= 0.163 Angle : 0.520 9.547 41212 Z= 0.270 Chirality : 0.039 0.163 4569 Planarity : 0.004 0.064 4876 Dihedral : 13.938 179.786 4767 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.17 % Allowed : 17.89 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.36 (0.15), residues: 3275 helix: 0.04 (0.16), residues: 1068 sheet: -0.97 (0.24), residues: 531 loop : -1.49 (0.15), residues: 1676 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6706.18 seconds wall clock time: 122 minutes 38.25 seconds (7358.25 seconds total)