Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 14:41:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3m_4404/05_2023/6i3m_4404_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3m_4404/05_2023/6i3m_4404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3m_4404/05_2023/6i3m_4404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3m_4404/05_2023/6i3m_4404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3m_4404/05_2023/6i3m_4404_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3m_4404/05_2023/6i3m_4404_updated.pdb" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 168 5.16 5 C 23570 2.51 5 N 6300 2.21 5 O 6972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D ARG 499": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 324": "NH1" <-> "NH2" Residue "G ARG 26": "NH1" <-> "NH2" Residue "G ARG 206": "NH1" <-> "NH2" Residue "G ARG 234": "NH1" <-> "NH2" Residue "G ARG 428": "NH1" <-> "NH2" Residue "I ARG 190": "NH1" <-> "NH2" Residue "I ARG 245": "NH1" <-> "NH2" Residue "J ARG 190": "NH1" <-> "NH2" Residue "J ARG 245": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H ARG 206": "NH1" <-> "NH2" Residue "H ARG 234": "NH1" <-> "NH2" Residue "H ARG 428": "NH1" <-> "NH2" Residue "F ARG 56": "NH1" <-> "NH2" Residue "F PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 324": "NH1" <-> "NH2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K GLU 209": "OE1" <-> "OE2" Residue "O GLU 231": "OE1" <-> "OE2" Residue "O GLU 383": "OE1" <-> "OE2" Residue "O GLU 494": "OE1" <-> "OE2" Residue "O GLU 506": "OE1" <-> "OE2" Residue "L ARG 53": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L GLU 209": "OE1" <-> "OE2" Residue "P GLU 231": "OE1" <-> "OE2" Residue "P GLU 383": "OE1" <-> "OE2" Residue "P GLU 494": "OE1" <-> "OE2" Residue "P GLU 506": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 37012 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2393 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "C" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2677 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "D" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2677 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "E" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2797 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Chain: "G" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3265 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 395} Chain: "I" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2187 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 3 Chain: "J" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2187 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 3 Chain: "B" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2393 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "H" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3265 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 395} Chain: "F" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2797 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Chain: "K" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2010 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain breaks: 2 Chain: "M" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "O" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3034 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2010 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain breaks: 2 Chain: "N" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "P" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3034 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 18.44, per 1000 atoms: 0.50 Number of scatterers: 37012 At special positions: 0 Unit cell: (296.14, 143.38, 121.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 2 15.00 O 6972 8.00 N 6300 7.00 C 23570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.99 Conformation dependent library (CDL) restraints added in 5.6 seconds 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8904 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 42 sheets defined 29.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 10 through 14 removed outlier: 3.824A pdb=" N LEU A 14 " --> pdb=" O TYR A 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 10 through 14' Processing helix chain 'A' and resid 22 through 36 removed outlier: 3.755A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 59 removed outlier: 4.196A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 81 removed outlier: 3.991A pdb=" N MET A 74 " --> pdb=" O CYS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 100 removed outlier: 4.425A pdb=" N ILE A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 116 removed outlier: 4.240A pdb=" N ARG A 109 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN A 110 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 112 " --> pdb=" O ARG A 109 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 114 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 removed outlier: 3.802A pdb=" N HIS A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 removed outlier: 3.742A pdb=" N LEU A 165 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR A 166 " --> pdb=" O ASN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 removed outlier: 4.107A pdb=" N VAL A 184 " --> pdb=" O ASP A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'C' and resid 272 through 282 Processing helix chain 'C' and resid 290 through 305 removed outlier: 4.147A pdb=" N ILE C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 333 removed outlier: 3.931A pdb=" N LEU C 329 " --> pdb=" O HIS C 325 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU C 330 " --> pdb=" O GLN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 removed outlier: 3.729A pdb=" N ALA C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 377 removed outlier: 4.710A pdb=" N GLU C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 393 removed outlier: 4.922A pdb=" N THR C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLN C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 417 Processing helix chain 'C' and resid 437 through 447 removed outlier: 3.526A pdb=" N THR C 443 " --> pdb=" O LYS C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 463 removed outlier: 5.000A pdb=" N ASP C 460 " --> pdb=" O THR C 457 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 462 " --> pdb=" O LEU C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 498 Processing helix chain 'C' and resid 637 through 646 Proline residue: C 641 - end of helix removed outlier: 4.126A pdb=" N GLU C 646 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 282 Processing helix chain 'D' and resid 290 through 305 removed outlier: 4.147A pdb=" N ILE D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 removed outlier: 3.931A pdb=" N LEU D 329 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU D 330 " --> pdb=" O GLN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 removed outlier: 3.729A pdb=" N ALA D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TRP D 346 " --> pdb=" O ASN D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 377 removed outlier: 4.710A pdb=" N GLU D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS D 370 " --> pdb=" O ASP D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 393 removed outlier: 4.922A pdb=" N THR D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLN D 393 " --> pdb=" O ASN D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 417 Processing helix chain 'D' and resid 437 through 447 removed outlier: 3.526A pdb=" N THR D 443 " --> pdb=" O LYS D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 463 removed outlier: 5.000A pdb=" N ASP D 460 " --> pdb=" O THR D 457 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 462 " --> pdb=" O LEU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 498 Processing helix chain 'D' and resid 637 through 646 Proline residue: D 641 - end of helix removed outlier: 4.126A pdb=" N GLU D 646 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 30 removed outlier: 3.682A pdb=" N ASP E 23 " --> pdb=" O ASN E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 54 removed outlier: 3.810A pdb=" N ALA E 54 " --> pdb=" O ARG E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.812A pdb=" N GLU E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU E 70 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY E 71 " --> pdb=" O ILE E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 106 removed outlier: 3.938A pdb=" N VAL E 87 " --> pdb=" O SER E 83 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE E 88 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU E 98 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU E 100 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 125 Processing helix chain 'E' and resid 147 through 167 removed outlier: 4.099A pdb=" N TYR E 150 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 153 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP E 160 " --> pdb=" O GLY E 157 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS E 166 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 175 Processing helix chain 'E' and resid 194 through 205 removed outlier: 4.304A pdb=" N ARG E 204 " --> pdb=" O LEU E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 278 through 287 removed outlier: 3.602A pdb=" N CYS E 282 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'E' and resid 362 through 368 Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 60 through 69 removed outlier: 4.268A pdb=" N PHE G 66 " --> pdb=" O TYR G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 91 removed outlier: 4.885A pdb=" N TYR G 89 " --> pdb=" O GLN G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 125 Processing helix chain 'G' and resid 145 through 158 removed outlier: 4.023A pdb=" N GLU G 150 " --> pdb=" O LYS G 147 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN G 158 " --> pdb=" O MET G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 248 removed outlier: 4.181A pdb=" N GLU G 248 " --> pdb=" O LEU G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 262 No H-bonds generated for 'chain 'G' and resid 259 through 262' Processing helix chain 'G' and resid 288 through 299 removed outlier: 4.847A pdb=" N THR G 293 " --> pdb=" O GLN G 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 83 removed outlier: 3.639A pdb=" N VAL I 80 " --> pdb=" O MET I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 127 removed outlier: 4.196A pdb=" N ALA I 125 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU I 126 " --> pdb=" O ILE I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 158 removed outlier: 4.102A pdb=" N LYS I 157 " --> pdb=" O GLU I 153 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU I 158 " --> pdb=" O SER I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 Processing helix chain 'I' and resid 258 through 261 No H-bonds generated for 'chain 'I' and resid 258 through 261' Processing helix chain 'I' and resid 282 through 286 Processing helix chain 'I' and resid 404 through 410 Processing helix chain 'J' and resid 76 through 83 removed outlier: 3.641A pdb=" N VAL J 80 " --> pdb=" O MET J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 127 removed outlier: 4.196A pdb=" N ALA J 125 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU J 126 " --> pdb=" O ILE J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 158 removed outlier: 4.102A pdb=" N LYS J 157 " --> pdb=" O GLU J 153 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU J 158 " --> pdb=" O SER J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 188 Processing helix chain 'J' and resid 258 through 261 No H-bonds generated for 'chain 'J' and resid 258 through 261' Processing helix chain 'J' and resid 282 through 286 Processing helix chain 'J' and resid 404 through 410 Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.825A pdb=" N LEU B 14 " --> pdb=" O TYR B 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 14' Processing helix chain 'B' and resid 22 through 36 removed outlier: 3.754A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 59 removed outlier: 4.196A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 81 removed outlier: 3.991A pdb=" N MET B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 100 removed outlier: 4.424A pdb=" N ILE B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 4.239A pdb=" N ARG B 109 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN B 110 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 112 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 144 removed outlier: 3.801A pdb=" N HIS B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.741A pdb=" N LEU B 165 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR B 166 " --> pdb=" O ASN B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 removed outlier: 4.107A pdb=" N VAL B 184 " --> pdb=" O ASP B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 292 through 301 Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 60 through 69 removed outlier: 4.267A pdb=" N PHE H 66 " --> pdb=" O TYR H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 91 removed outlier: 4.886A pdb=" N TYR H 89 " --> pdb=" O GLN H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 125 Processing helix chain 'H' and resid 145 through 158 removed outlier: 4.024A pdb=" N GLU H 150 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN H 158 " --> pdb=" O MET H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 248 removed outlier: 4.181A pdb=" N GLU H 248 " --> pdb=" O LEU H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 262 No H-bonds generated for 'chain 'H' and resid 259 through 262' Processing helix chain 'H' and resid 288 through 299 removed outlier: 4.847A pdb=" N THR H 293 " --> pdb=" O GLN H 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 30 removed outlier: 3.682A pdb=" N ASP F 23 " --> pdb=" O ASN F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 54 removed outlier: 3.810A pdb=" N ALA F 54 " --> pdb=" O ARG F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 77 removed outlier: 3.812A pdb=" N GLU F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU F 70 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY F 71 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 106 removed outlier: 3.938A pdb=" N VAL F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE F 88 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU F 98 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU F 100 " --> pdb=" O ARG F 96 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER F 105 " --> pdb=" O GLU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 125 Processing helix chain 'F' and resid 147 through 167 removed outlier: 4.100A pdb=" N TYR F 150 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL F 153 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP F 160 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS F 166 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 175 Processing helix chain 'F' and resid 194 through 205 removed outlier: 4.304A pdb=" N ARG F 204 " --> pdb=" O LEU F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 224 No H-bonds generated for 'chain 'F' and resid 222 through 224' Processing helix chain 'F' and resid 226 through 235 Processing helix chain 'F' and resid 278 through 287 removed outlier: 3.602A pdb=" N CYS F 282 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU F 283 " --> pdb=" O SER F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 358 through 360 No H-bonds generated for 'chain 'F' and resid 358 through 360' Processing helix chain 'F' and resid 362 through 368 Processing helix chain 'K' and resid 58 through 64 removed outlier: 4.144A pdb=" N ILE K 63 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG K 64 " --> pdb=" O GLN K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 119 removed outlier: 3.770A pdb=" N ILE K 96 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU K 112 " --> pdb=" O VAL K 108 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N CYS K 115 " --> pdb=" O ILE K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 137 Proline residue: K 133 - end of helix Processing helix chain 'K' and resid 141 through 148 removed outlier: 3.668A pdb=" N LEU K 147 " --> pdb=" O GLU K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 157 Processing helix chain 'K' and resid 164 through 172 Processing helix chain 'K' and resid 197 through 208 removed outlier: 3.604A pdb=" N SER K 207 " --> pdb=" O ASP K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 257 removed outlier: 3.560A pdb=" N GLU K 245 " --> pdb=" O ILE K 241 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER K 246 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR K 256 " --> pdb=" O THR K 252 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS K 257 " --> pdb=" O GLU K 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 140 Processing helix chain 'O' and resid 113 through 121 Processing helix chain 'O' and resid 131 through 134 No H-bonds generated for 'chain 'O' and resid 131 through 134' Processing helix chain 'O' and resid 202 through 208 Processing helix chain 'O' and resid 227 through 238 Processing helix chain 'O' and resid 258 through 269 Processing helix chain 'O' and resid 291 through 300 Processing helix chain 'L' and resid 58 through 64 removed outlier: 4.144A pdb=" N ILE L 63 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG L 64 " --> pdb=" O GLN L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 119 removed outlier: 3.770A pdb=" N ILE L 96 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE L 111 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU L 112 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N CYS L 115 " --> pdb=" O ILE L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 137 Proline residue: L 133 - end of helix Processing helix chain 'L' and resid 141 through 148 removed outlier: 3.669A pdb=" N LEU L 147 " --> pdb=" O GLU L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 157 Processing helix chain 'L' and resid 164 through 172 Processing helix chain 'L' and resid 197 through 208 removed outlier: 3.602A pdb=" N SER L 207 " --> pdb=" O ASP L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 257 removed outlier: 3.560A pdb=" N GLU L 245 " --> pdb=" O ILE L 241 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER L 246 " --> pdb=" O GLU L 242 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR L 256 " --> pdb=" O THR L 252 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 140 Processing helix chain 'P' and resid 113 through 121 Processing helix chain 'P' and resid 131 through 134 No H-bonds generated for 'chain 'P' and resid 131 through 134' Processing helix chain 'P' and resid 202 through 208 Processing helix chain 'P' and resid 227 through 238 Processing helix chain 'P' and resid 258 through 269 Processing helix chain 'P' and resid 291 through 300 Processing sheet with id= A, first strand: chain 'A' and resid 124 through 128 Processing sheet with id= B, first strand: chain 'A' and resid 193 through 196 removed outlier: 7.897A pdb=" N VAL A 196 " --> pdb=" O PRO A 226 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR A 228 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA A 282 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 288 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 398 through 401 Processing sheet with id= D, first strand: chain 'C' and resid 470 through 473 removed outlier: 6.923A pdb=" N LYS C 627 " --> pdb=" O VAL C 505 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 398 through 401 Processing sheet with id= F, first strand: chain 'D' and resid 470 through 473 removed outlier: 6.923A pdb=" N LYS D 627 " --> pdb=" O VAL D 505 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 291 through 295 removed outlier: 3.596A pdb=" N THR E 216 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU E 241 " --> pdb=" O VAL E 215 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 349 through 351 Processing sheet with id= I, first strand: chain 'G' and resid 28 through 32 removed outlier: 3.682A pdb=" N ILE G 133 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 74 through 79 removed outlier: 7.180A pdb=" N LYS G 103 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LEU G 77 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR G 105 " --> pdb=" O LEU G 77 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N CYS G 79 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE G 107 " --> pdb=" O CYS G 79 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'G' and resid 139 through 141 Processing sheet with id= L, first strand: chain 'G' and resid 164 through 166 Processing sheet with id= M, first strand: chain 'G' and resid 185 through 188 removed outlier: 3.879A pdb=" N ARG G 227 " --> pdb=" O PHE G 185 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 325 through 327 removed outlier: 6.678A pdb=" N THR G 343 " --> pdb=" O TYR G 326 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 356 through 358 Processing sheet with id= P, first strand: chain 'B' and resid 124 through 128 Processing sheet with id= Q, first strand: chain 'B' and resid 193 through 196 removed outlier: 7.898A pdb=" N VAL B 196 " --> pdb=" O PRO B 226 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR B 228 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA B 282 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 288 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 28 through 32 removed outlier: 3.681A pdb=" N ILE H 133 " --> pdb=" O GLN H 28 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 74 through 79 removed outlier: 7.180A pdb=" N LYS H 103 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LEU H 77 " --> pdb=" O LYS H 103 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR H 105 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N CYS H 79 " --> pdb=" O THR H 105 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE H 107 " --> pdb=" O CYS H 79 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'H' and resid 139 through 141 Processing sheet with id= U, first strand: chain 'H' and resid 164 through 166 Processing sheet with id= V, first strand: chain 'H' and resid 185 through 188 removed outlier: 3.879A pdb=" N ARG H 227 " --> pdb=" O PHE H 185 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 325 through 327 removed outlier: 6.678A pdb=" N THR H 343 " --> pdb=" O TYR H 326 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'H' and resid 356 through 358 Processing sheet with id= Y, first strand: chain 'F' and resid 291 through 295 removed outlier: 3.596A pdb=" N THR F 216 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU F 241 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 349 through 351 Processing sheet with id= AA, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= AB, first strand: chain 'K' and resid 182 through 189 Processing sheet with id= AC, first strand: chain 'O' and resid 280 through 282 removed outlier: 8.443A pdb=" N VAL O 281 " --> pdb=" O VAL O 244 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE O 246 " --> pdb=" O VAL O 281 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALA O 214 " --> pdb=" O ILE O 245 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU O 247 " --> pdb=" O ALA O 214 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU O 216 " --> pdb=" O LEU O 247 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE O 103 " --> pdb=" O HIS O 188 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER O 190 " --> pdb=" O ILE O 103 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N THR O 105 " --> pdb=" O SER O 190 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL O 192 " --> pdb=" O THR O 105 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLY O 107 " --> pdb=" O VAL O 192 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE O 147 " --> pdb=" O VAL O 186 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N HIS O 188 " --> pdb=" O ALA O 145 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA O 145 " --> pdb=" O HIS O 188 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 373 through 376 removed outlier: 4.296A pdb=" N ASN O 344 " --> pdb=" O ARG O 314 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE O 316 " --> pdb=" O ILE O 342 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE O 342 " --> pdb=" O ILE O 316 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY O 394 " --> pdb=" O ILE O 342 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU O 380 " --> pdb=" O LEU O 387 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU O 387 " --> pdb=" O LEU O 380 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA O 382 " --> pdb=" O ASN O 385 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'O' and resid 319 through 322 Processing sheet with id= AF, first strand: chain 'O' and resid 425 through 427 Processing sheet with id= AG, first strand: chain 'O' and resid 482 through 486 removed outlier: 3.944A pdb=" N GLY O 513 " --> pdb=" O LEU O 501 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG O 484 " --> pdb=" O VAL O 476 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'O' and resid 502 through 504 Processing sheet with id= AI, first strand: chain 'L' and resid 19 through 23 Processing sheet with id= AJ, first strand: chain 'L' and resid 182 through 189 Processing sheet with id= AK, first strand: chain 'P' and resid 280 through 282 removed outlier: 8.444A pdb=" N VAL P 281 " --> pdb=" O VAL P 244 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE P 246 " --> pdb=" O VAL P 281 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA P 214 " --> pdb=" O ILE P 245 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU P 247 " --> pdb=" O ALA P 214 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU P 216 " --> pdb=" O LEU P 247 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE P 103 " --> pdb=" O HIS P 188 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N SER P 190 " --> pdb=" O ILE P 103 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N THR P 105 " --> pdb=" O SER P 190 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL P 192 " --> pdb=" O THR P 105 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLY P 107 " --> pdb=" O VAL P 192 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE P 147 " --> pdb=" O VAL P 186 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N HIS P 188 " --> pdb=" O ALA P 145 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA P 145 " --> pdb=" O HIS P 188 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'P' and resid 373 through 376 removed outlier: 4.295A pdb=" N ASN P 344 " --> pdb=" O ARG P 314 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE P 316 " --> pdb=" O ILE P 342 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE P 342 " --> pdb=" O ILE P 316 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY P 394 " --> pdb=" O ILE P 342 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU P 380 " --> pdb=" O LEU P 387 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU P 387 " --> pdb=" O LEU P 380 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA P 382 " --> pdb=" O ASN P 385 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'P' and resid 319 through 322 Processing sheet with id= AN, first strand: chain 'P' and resid 425 through 427 Processing sheet with id= AO, first strand: chain 'P' and resid 482 through 486 removed outlier: 3.942A pdb=" N GLY P 513 " --> pdb=" O LEU P 501 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG P 484 " --> pdb=" O VAL P 476 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'P' and resid 502 through 504 948 hydrogen bonds defined for protein. 2526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.88 Time building geometry restraints manager: 15.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11354 1.34 - 1.46: 6037 1.46 - 1.58: 19997 1.58 - 1.70: 8 1.70 - 1.82: 254 Bond restraints: 37650 Sorted by residual: bond pdb=" CA VAL O 453 " pdb=" CB VAL O 453 " ideal model delta sigma weight residual 1.530 1.562 -0.032 1.05e-02 9.07e+03 9.23e+00 bond pdb=" CZ ARG P 503 " pdb=" NH1 ARG P 503 " ideal model delta sigma weight residual 1.323 1.365 -0.042 1.40e-02 5.10e+03 8.95e+00 bond pdb=" CZ ARG O 503 " pdb=" NH1 ARG O 503 " ideal model delta sigma weight residual 1.323 1.364 -0.041 1.40e-02 5.10e+03 8.75e+00 bond pdb=" CA VAL P 453 " pdb=" CB VAL P 453 " ideal model delta sigma weight residual 1.530 1.561 -0.031 1.05e-02 9.07e+03 8.57e+00 bond pdb=" C CYS O 194 " pdb=" N PRO O 195 " ideal model delta sigma weight residual 1.333 1.366 -0.033 1.17e-02 7.31e+03 8.20e+00 ... (remaining 37645 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.62: 763 105.62 - 112.82: 19384 112.82 - 120.02: 14441 120.02 - 127.21: 16025 127.21 - 134.41: 339 Bond angle restraints: 50952 Sorted by residual: angle pdb=" N THR E 109 " pdb=" CA THR E 109 " pdb=" C THR E 109 " ideal model delta sigma weight residual 111.07 120.32 -9.25 1.07e+00 8.73e-01 7.47e+01 angle pdb=" N THR F 109 " pdb=" CA THR F 109 " pdb=" C THR F 109 " ideal model delta sigma weight residual 111.07 120.29 -9.22 1.07e+00 8.73e-01 7.42e+01 angle pdb=" N ILE E 238 " pdb=" CA ILE E 238 " pdb=" C ILE E 238 " ideal model delta sigma weight residual 106.21 113.48 -7.27 1.07e+00 8.73e-01 4.61e+01 angle pdb=" N ILE F 238 " pdb=" CA ILE F 238 " pdb=" C ILE F 238 " ideal model delta sigma weight residual 106.21 113.47 -7.26 1.07e+00 8.73e-01 4.60e+01 angle pdb=" C GLU F 115 " pdb=" N PRO F 116 " pdb=" CA PRO F 116 " ideal model delta sigma weight residual 119.05 126.40 -7.35 1.11e+00 8.12e-01 4.38e+01 ... (remaining 50947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 20763 16.20 - 32.39: 1685 32.39 - 48.59: 478 48.59 - 64.79: 80 64.79 - 80.99: 54 Dihedral angle restraints: 23060 sinusoidal: 9368 harmonic: 13692 Sorted by residual: dihedral pdb=" CA ARG H 178 " pdb=" C ARG H 178 " pdb=" N THR H 179 " pdb=" CA THR H 179 " ideal model delta harmonic sigma weight residual -180.00 -134.64 -45.36 0 5.00e+00 4.00e-02 8.23e+01 dihedral pdb=" CA ARG G 178 " pdb=" C ARG G 178 " pdb=" N THR G 179 " pdb=" CA THR G 179 " ideal model delta harmonic sigma weight residual -180.00 -134.65 -45.35 0 5.00e+00 4.00e-02 8.22e+01 dihedral pdb=" CA HIS K 140 " pdb=" C HIS K 140 " pdb=" N ALA K 141 " pdb=" CA ALA K 141 " ideal model delta harmonic sigma weight residual -180.00 -144.25 -35.75 0 5.00e+00 4.00e-02 5.11e+01 ... (remaining 23057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 5446 0.122 - 0.243: 472 0.243 - 0.365: 38 0.365 - 0.487: 0 0.487 - 0.608: 2 Chirality restraints: 5958 Sorted by residual: chirality pdb=" CA ARG P 356 " pdb=" N ARG P 356 " pdb=" C ARG P 356 " pdb=" CB ARG P 356 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.25e+00 chirality pdb=" CA ARG O 356 " pdb=" N ARG O 356 " pdb=" C ARG O 356 " pdb=" CB ARG O 356 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.24e+00 chirality pdb=" CA ASP P 130 " pdb=" N ASP P 130 " pdb=" C ASP P 130 " pdb=" CB ASP P 130 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 5955 not shown) Planarity restraints: 6490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 181 " -0.051 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO H 182 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO H 182 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO H 182 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 181 " 0.051 5.00e-02 4.00e+02 7.83e-02 9.81e+00 pdb=" N PRO G 182 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO G 182 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO G 182 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 341 " 0.046 5.00e-02 4.00e+02 6.99e-02 7.81e+00 pdb=" N PRO E 342 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 342 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 342 " 0.038 5.00e-02 4.00e+02 ... (remaining 6487 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3109 2.74 - 3.28: 36171 3.28 - 3.82: 60609 3.82 - 4.36: 71483 4.36 - 4.90: 117858 Nonbonded interactions: 289230 Sorted by model distance: nonbonded pdb=" O GLY E 269 " pdb=" OH TYR E 349 " model vdw 2.201 2.440 nonbonded pdb=" O GLY F 269 " pdb=" OH TYR F 349 " model vdw 2.202 2.440 nonbonded pdb=" OG SER E 37 " pdb=" OG SER E 83 " model vdw 2.302 2.440 nonbonded pdb=" OG SER F 37 " pdb=" OG SER F 83 " model vdw 2.302 2.440 nonbonded pdb=" OG SER H 169 " pdb=" O ALA H 282 " model vdw 2.304 2.440 ... (remaining 289225 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 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: 0.030 Extract box with map and model: 10.920 Check model and map are aligned: 0.530 Set scattering table: 0.310 Process input model: 87.730 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.270 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.071 37650 Z= 0.467 Angle : 1.240 13.376 50952 Z= 0.712 Chirality : 0.073 0.608 5958 Planarity : 0.007 0.078 6490 Dihedral : 13.811 80.985 14156 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.25 % Favored : 88.40 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.16 (0.10), residues: 4604 helix: -2.65 (0.11), residues: 1376 sheet: -2.53 (0.19), residues: 592 loop : -2.98 (0.11), residues: 2636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 669 time to evaluate : 4.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 10 residues processed: 768 average time/residue: 0.5220 time to fit residues: 633.0848 Evaluate side-chains 362 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 352 time to evaluate : 4.622 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3316 time to fit residues: 12.7264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 388 optimal weight: 9.9990 chunk 348 optimal weight: 5.9990 chunk 193 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 360 optimal weight: 8.9990 chunk 139 optimal weight: 0.3980 chunk 219 optimal weight: 7.9990 chunk 268 optimal weight: 0.9980 chunk 417 optimal weight: 10.0000 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 HIS C 373 GLN ** C 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN C 446 ASN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 HIS D 373 GLN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 HIS E 227 HIS ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 ASN G 96 ASN ** G 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 ASN I 118 GLN ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 GLN ** I 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 118 GLN ** J 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 309 GLN ** J 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 ASN H 96 ASN ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 371 ASN F 78 HIS F 227 HIS K 103 GLN O 221 ASN O 433 ASN L 103 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 37650 Z= 0.337 Angle : 0.774 14.661 50952 Z= 0.403 Chirality : 0.050 0.318 5958 Planarity : 0.006 0.065 6490 Dihedral : 7.280 78.395 5028 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.58 % Favored : 90.33 % Rotamer Outliers : 4.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.29 (0.11), residues: 4604 helix: -1.56 (0.13), residues: 1416 sheet: -2.17 (0.19), residues: 652 loop : -2.62 (0.12), residues: 2536 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 404 time to evaluate : 4.491 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: 169 outliers final: 75 residues processed: 546 average time/residue: 0.4668 time to fit residues: 426.2212 Evaluate side-chains 402 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 327 time to evaluate : 4.149 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.3378 time to fit residues: 53.6443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 232 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 347 optimal weight: 50.0000 chunk 284 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 418 optimal weight: 7.9990 chunk 452 optimal weight: 10.0000 chunk 372 optimal weight: 0.0000 chunk 414 optimal weight: 20.0000 chunk 142 optimal weight: 0.0030 chunk 335 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN G 393 HIS ** I 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 393 HIS O 508 HIS P 248 GLN P 262 HIS P 422 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 37650 Z= 0.175 Angle : 0.677 11.735 50952 Z= 0.345 Chirality : 0.047 0.308 5958 Planarity : 0.005 0.053 6490 Dihedral : 6.532 75.679 5028 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.58 % Favored : 91.33 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.12), residues: 4604 helix: -1.20 (0.13), residues: 1410 sheet: -2.09 (0.19), residues: 658 loop : -2.41 (0.12), residues: 2536 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 426 time to evaluate : 4.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 21 residues processed: 505 average time/residue: 0.4704 time to fit residues: 399.2361 Evaluate side-chains 370 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 349 time to evaluate : 4.875 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3293 time to fit residues: 19.4081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 413 optimal weight: 10.0000 chunk 314 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 281 optimal weight: 4.9990 chunk 419 optimal weight: 20.0000 chunk 444 optimal weight: 40.0000 chunk 219 optimal weight: 8.9990 chunk 398 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN ** D 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS G 85 GLN ** G 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 215 GLN ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 215 GLN ** J 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 212 GLN O 248 GLN O 290 ASN ** P 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 37650 Z= 0.406 Angle : 0.775 10.451 50952 Z= 0.400 Chirality : 0.050 0.274 5958 Planarity : 0.005 0.057 6490 Dihedral : 6.721 72.969 5028 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.73 % Favored : 89.18 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.12), residues: 4604 helix: -1.03 (0.13), residues: 1386 sheet: -2.11 (0.19), residues: 678 loop : -2.34 (0.12), residues: 2540 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 370 time to evaluate : 4.224 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: 129 outliers final: 71 residues processed: 466 average time/residue: 0.4545 time to fit residues: 358.8592 Evaluate side-chains 404 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 333 time to evaluate : 4.769 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.3288 time to fit residues: 51.2187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 370 optimal weight: 30.0000 chunk 252 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 331 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 379 optimal weight: 50.0000 chunk 307 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 399 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 384 GLN ** C 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 GLN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN ** G 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS J 293 GLN H 92 ASN ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN O 248 GLN O 422 HIS L 103 GLN ** P 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 221 ASN ** P 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 37650 Z= 0.265 Angle : 0.691 10.312 50952 Z= 0.351 Chirality : 0.047 0.191 5958 Planarity : 0.005 0.078 6490 Dihedral : 6.380 71.566 5028 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.14 % Favored : 90.77 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.12), residues: 4604 helix: -0.76 (0.14), residues: 1354 sheet: -2.12 (0.18), residues: 688 loop : -2.24 (0.12), residues: 2562 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 368 time to evaluate : 4.623 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: 74 outliers final: 34 residues processed: 426 average time/residue: 0.4789 time to fit residues: 345.0537 Evaluate side-chains 386 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 352 time to evaluate : 4.039 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3097 time to fit residues: 25.7742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 149 optimal weight: 3.9990 chunk 400 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 445 optimal weight: 30.0000 chunk 369 optimal weight: 7.9990 chunk 206 optimal weight: 0.0570 chunk 37 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 233 optimal weight: 0.9980 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: