Starting phenix.real_space_refine on Tue Apr 16 02:14:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3m_4404/04_2024/6i3m_4404_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3m_4404/04_2024/6i3m_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_4404/04_2024/6i3m_4404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3m_4404/04_2024/6i3m_4404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3m_4404/04_2024/6i3m_4404_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3m_4404/04_2024/6i3m_4404_updated.pdb" } resolution = 3.93 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= 0.008 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 18.11, per 1000 atoms: 0.49 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: 13.36 Conformation dependent library (CDL) restraints added in 6.4 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: 6.58 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: 12.61 Time building geometry restraints manager: 14.64 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.450 Check model and map are aligned: 0.490 Set scattering table: 0.310 Process input model: 91.850 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.240 ------------------------------------------------------------------------------- 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 % Allowed : 8.25 % Favored : 88.92 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP K 132 HIS 0.010 0.002 HIS A 234 PHE 0.038 0.003 PHE J 119 TYR 0.038 0.003 TYR K 9 ARG 0.011 0.001 ARG E 324 *********************** 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 : 4.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7820 (tpt) cc_final: 0.7499 (tpt) REVERT: A 78 LEU cc_start: 0.8431 (tt) cc_final: 0.7900 (mm) REVERT: A 214 TYR cc_start: 0.9239 (t80) cc_final: 0.8744 (t80) REVERT: A 264 GLU cc_start: 0.8128 (tp30) cc_final: 0.7626 (mm-30) REVERT: A 277 GLN cc_start: 0.8443 (pp30) cc_final: 0.8197 (pt0) REVERT: C 274 ILE cc_start: 0.9057 (tt) cc_final: 0.8828 (tt) REVERT: C 296 MET cc_start: 0.8361 (tmm) cc_final: 0.7959 (tmm) REVERT: C 317 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.8056 (ttm110) REVERT: C 319 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8696 (tt) REVERT: C 326 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8054 (mm-40) REVERT: C 364 LYS cc_start: 0.8334 (mttt) cc_final: 0.8133 (mtpt) REVERT: C 383 ASP cc_start: 0.8045 (m-30) cc_final: 0.7675 (m-30) REVERT: C 384 GLN cc_start: 0.8385 (tp-100) cc_final: 0.8030 (tp-100) REVERT: D 296 MET cc_start: 0.8332 (tmm) cc_final: 0.8116 (tmm) REVERT: D 317 ARG cc_start: 0.8334 (mtt-85) cc_final: 0.8096 (ttm110) REVERT: D 326 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8003 (mm-40) REVERT: D 383 ASP cc_start: 0.8057 (m-30) cc_final: 0.7658 (m-30) REVERT: D 384 GLN cc_start: 0.8393 (tp-100) cc_final: 0.8048 (tp-100) REVERT: D 402 THR cc_start: 0.9267 (p) cc_final: 0.9045 (m) REVERT: E 97 ASP cc_start: 0.8307 (t0) cc_final: 0.7728 (t0) REVERT: E 127 LYS cc_start: 0.5971 (mmpt) cc_final: 0.5648 (tptp) REVERT: E 144 MET cc_start: 0.3755 (ttm) cc_final: 0.3292 (tpp) REVERT: E 289 ARG cc_start: 0.8612 (mmt-90) cc_final: 0.8315 (mpt180) REVERT: G 26 ARG cc_start: 0.8055 (mpt180) cc_final: 0.7250 (ptt-90) REVERT: G 294 ILE cc_start: 0.9108 (pt) cc_final: 0.8716 (mt) REVERT: I 80 VAL cc_start: 0.5961 (m) cc_final: 0.5671 (m) REVERT: I 174 PHE cc_start: 0.6807 (t80) cc_final: 0.6442 (t80) REVERT: I 200 TYR cc_start: 0.5710 (m-10) cc_final: 0.5449 (m-10) REVERT: I 399 ASN cc_start: 0.2247 (p0) cc_final: 0.1922 (p0) REVERT: J 197 MET cc_start: 0.6575 (ptm) cc_final: 0.6277 (ppp) REVERT: J 199 ILE cc_start: 0.6747 (tp) cc_final: 0.6367 (tp) REVERT: J 200 TYR cc_start: 0.5640 (m-10) cc_final: 0.5401 (m-10) REVERT: J 393 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.6900 (pp) REVERT: J 394 ARG cc_start: 0.4454 (mtm180) cc_final: 0.4183 (mmp80) REVERT: J 399 ASN cc_start: 0.2711 (p0) cc_final: 0.2410 (p0) REVERT: B 74 MET cc_start: 0.7806 (tpt) cc_final: 0.7056 (tpt) REVERT: B 78 LEU cc_start: 0.8350 (tt) cc_final: 0.7742 (mm) REVERT: B 264 GLU cc_start: 0.8015 (tp30) cc_final: 0.7544 (mm-30) REVERT: B 277 GLN cc_start: 0.8417 (pp30) cc_final: 0.8098 (pt0) REVERT: H 26 ARG cc_start: 0.7852 (mpt180) cc_final: 0.7153 (ptt-90) REVERT: H 294 ILE cc_start: 0.9168 (pt) cc_final: 0.8733 (mt) REVERT: H 413 ILE cc_start: 0.8667 (mt) cc_final: 0.8424 (mm) REVERT: F 97 ASP cc_start: 0.8351 (t0) cc_final: 0.7772 (t0) REVERT: F 127 LYS cc_start: 0.6131 (mmpt) cc_final: 0.5816 (tptp) REVERT: F 144 MET cc_start: 0.3696 (ttm) cc_final: 0.3233 (tpp) REVERT: F 289 ARG cc_start: 0.8606 (mmt-90) cc_final: 0.8291 (mpt180) REVERT: K 23 ASN cc_start: 0.7700 (p0) cc_final: 0.7179 (p0) REVERT: K 171 ASN cc_start: 0.8166 (t0) cc_final: 0.7901 (m-40) REVERT: O 192 VAL cc_start: 0.2765 (OUTLIER) cc_final: 0.2226 (t) REVERT: O 201 MET cc_start: 0.1527 (mmm) cc_final: -0.1342 (ppp) REVERT: O 257 GLU cc_start: 0.2332 (OUTLIER) cc_final: 0.1236 (pt0) REVERT: O 354 GLU cc_start: 0.0932 (OUTLIER) cc_final: 0.0187 (tt0) REVERT: O 476 VAL cc_start: 0.0629 (t) cc_final: 0.0126 (t) REVERT: L 119 PHE cc_start: 0.6509 (t80) cc_final: 0.6047 (t80) REVERT: P 192 VAL cc_start: 0.2238 (OUTLIER) cc_final: 0.1610 (t) REVERT: P 201 MET cc_start: 0.0791 (mmm) cc_final: -0.1973 (ttp) REVERT: P 354 GLU cc_start: 0.0948 (OUTLIER) cc_final: -0.0088 (tt0) REVERT: P 463 MET cc_start: 0.3110 (ttp) cc_final: 0.2793 (ttm) outliers start: 118 outliers final: 10 residues processed: 768 average time/residue: 0.5431 time to fit residues: 654.8505 Evaluate side-chains 385 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 368 time to evaluate : 4.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain J residue 393 ILE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 192 VAL Chi-restraints excluded: chain O residue 228 GLN Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 354 GLU Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 236 ILE Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 432 ILE 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: 2.9990 chunk 119 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 360 optimal weight: 2.9990 chunk 139 optimal weight: 0.3980 chunk 219 optimal weight: 9.9990 chunk 268 optimal weight: 0.9980 chunk 417 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 GLN C 389 ASN C 416 ASN C 446 ASN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN D 389 ASN D 416 ASN ** D 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 HIS E 227 HIS G 85 GLN 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 433 ASN L 103 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 37650 Z= 0.326 Angle : 0.758 14.109 50952 Z= 0.395 Chirality : 0.049 0.303 5958 Planarity : 0.006 0.065 6490 Dihedral : 7.719 78.037 5062 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.56 % Favored : 90.36 % Rotamer: Outliers : 4.01 % Allowed : 13.05 % Favored : 82.94 % 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: -3.25 (0.12), residues: 4604 helix: -1.51 (0.13), residues: 1414 sheet: -2.17 (0.19), residues: 652 loop : -2.60 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 132 HIS 0.007 0.002 HIS A 93 PHE 0.025 0.002 PHE A 149 TYR 0.019 0.002 TYR C 624 ARG 0.015 0.001 ARG I 234 *********************** 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 600 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 433 time to evaluate : 4.206 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: A 24 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7968 (pt) REVERT: A 74 MET cc_start: 0.7955 (tpt) cc_final: 0.7642 (tpt) REVERT: A 78 LEU cc_start: 0.8607 (tt) cc_final: 0.7982 (mm) REVERT: A 100 LEU cc_start: 0.7519 (mt) cc_final: 0.7265 (tt) REVERT: A 214 TYR cc_start: 0.9262 (t80) cc_final: 0.8817 (t80) REVERT: A 277 GLN cc_start: 0.8509 (pp30) cc_final: 0.8282 (pt0) REVERT: C 317 ARG cc_start: 0.8419 (mtt-85) cc_final: 0.7932 (mtm110) REVERT: C 319 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8710 (tt) REVERT: C 383 ASP cc_start: 0.8283 (m-30) cc_final: 0.7973 (m-30) REVERT: C 384 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7490 (tp-100) REVERT: D 317 ARG cc_start: 0.8500 (mtt-85) cc_final: 0.8182 (ttm110) REVERT: D 326 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8258 (mm-40) REVERT: D 383 ASP cc_start: 0.8300 (m-30) cc_final: 0.7980 (m-30) REVERT: D 384 GLN cc_start: 0.8071 (tp-100) cc_final: 0.7487 (tp-100) REVERT: D 635 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9180 (pp) REVERT: E 104 MET cc_start: 0.2993 (ptt) cc_final: 0.2621 (ptt) REVERT: E 144 MET cc_start: 0.3548 (ttm) cc_final: 0.3041 (tpp) REVERT: E 289 ARG cc_start: 0.8688 (mmt-90) cc_final: 0.8366 (mpt180) REVERT: G 26 ARG cc_start: 0.7941 (mpt180) cc_final: 0.7643 (mpt90) REVERT: G 47 LYS cc_start: 0.8887 (ptpp) cc_final: 0.8600 (ptmt) REVERT: G 162 HIS cc_start: 0.7295 (p90) cc_final: 0.6864 (p90) REVERT: G 163 ILE cc_start: 0.8739 (mm) cc_final: 0.8492 (mm) REVERT: G 288 TRP cc_start: 0.8649 (m100) cc_final: 0.8207 (m100) REVERT: G 294 ILE cc_start: 0.9179 (pt) cc_final: 0.8741 (mm) REVERT: I 174 PHE cc_start: 0.6760 (t80) cc_final: 0.6425 (t80) REVERT: I 399 ASN cc_start: 0.2357 (p0) cc_final: 0.1952 (p0) REVERT: J 6 PHE cc_start: 0.5452 (t80) cc_final: 0.5226 (t80) REVERT: J 115 ARG cc_start: 0.2561 (tpp-160) cc_final: 0.0300 (tmm160) REVERT: J 174 PHE cc_start: 0.6878 (t80) cc_final: 0.6620 (t80) REVERT: J 197 MET cc_start: 0.7054 (ptm) cc_final: 0.6307 (ppp) REVERT: J 399 ASN cc_start: 0.2504 (p0) cc_final: 0.2110 (p0) REVERT: B 24 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8064 (pt) REVERT: B 78 LEU cc_start: 0.8564 (tt) cc_final: 0.7837 (mm) REVERT: B 277 GLN cc_start: 0.8449 (pp30) cc_final: 0.7938 (pp30) REVERT: H 26 ARG cc_start: 0.7765 (mpt180) cc_final: 0.7458 (mpt90) REVERT: H 47 LYS cc_start: 0.8929 (ptpp) cc_final: 0.8693 (ptmt) REVERT: H 212 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7029 (mm-40) REVERT: H 288 TRP cc_start: 0.8694 (m100) cc_final: 0.8210 (m100) REVERT: H 294 ILE cc_start: 0.9285 (pt) cc_final: 0.8774 (mm) REVERT: F 104 MET cc_start: 0.2988 (ptt) cc_final: 0.2614 (ptt) REVERT: F 127 LYS cc_start: 0.6083 (mmpt) cc_final: 0.5868 (tptt) REVERT: F 144 MET cc_start: 0.3704 (ttm) cc_final: 0.3319 (tpp) REVERT: F 150 TYR cc_start: 0.8685 (m-80) cc_final: 0.8466 (m-10) REVERT: F 289 ARG cc_start: 0.8700 (mmt-90) cc_final: 0.8346 (mpt180) REVERT: K 171 ASN cc_start: 0.8084 (t0) cc_final: 0.7845 (m-40) REVERT: O 201 MET cc_start: 0.2851 (mmm) cc_final: -0.0415 (ppp) REVERT: O 257 GLU cc_start: 0.2702 (OUTLIER) cc_final: 0.1281 (pt0) REVERT: O 354 GLU cc_start: 0.1125 (OUTLIER) cc_final: -0.0179 (tt0) REVERT: O 428 THR cc_start: 0.0708 (OUTLIER) cc_final: -0.0045 (t) REVERT: L 21 MET cc_start: 0.8390 (ttm) cc_final: 0.8067 (tpp) REVERT: P 201 MET cc_start: 0.2077 (mmm) cc_final: -0.1402 (ttp) REVERT: P 354 GLU cc_start: 0.1636 (OUTLIER) cc_final: 0.0014 (tt0) REVERT: P 428 THR cc_start: 0.2464 (OUTLIER) cc_final: 0.1737 (t) REVERT: P 455 LYS cc_start: 0.4640 (mttm) cc_final: 0.4153 (mptt) outliers start: 167 outliers final: 72 residues processed: 574 average time/residue: 0.4715 time to fit residues: 449.1665 Evaluate side-chains 426 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 344 time to evaluate : 4.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 645 ARG Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 66 PHE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 212 GLN Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain K residue 45 MET Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 111 HIS Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 354 GLU Chi-restraints excluded: chain O residue 373 ILE Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 426 ILE Chi-restraints excluded: chain O residue 428 THR Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 373 ILE Chi-restraints excluded: chain P residue 400 THR Chi-restraints excluded: chain P residue 426 ILE Chi-restraints excluded: chain P residue 428 THR Chi-restraints excluded: chain P residue 496 ASN Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 232 optimal weight: 0.0370 chunk 129 optimal weight: 0.7980 chunk 347 optimal weight: 40.0000 chunk 284 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 418 optimal weight: 4.9990 chunk 452 optimal weight: 8.9990 chunk 372 optimal weight: 10.0000 chunk 414 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 335 optimal weight: 3.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN G 393 HIS I 215 GLN ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 393 HIS ** O 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 508 HIS P 262 HIS P 422 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 37650 Z= 0.231 Angle : 0.682 9.744 50952 Z= 0.350 Chirality : 0.047 0.307 5958 Planarity : 0.005 0.053 6490 Dihedral : 6.880 74.682 5044 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.47 % Favored : 90.44 % Rotamer: Outliers : 3.77 % Allowed : 15.31 % Favored : 80.93 % 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: -2.88 (0.12), residues: 4604 helix: -1.10 (0.13), residues: 1418 sheet: -2.05 (0.19), residues: 648 loop : -2.40 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 132 HIS 0.005 0.001 HIS B 93 PHE 0.022 0.002 PHE I 223 TYR 0.022 0.002 TYR K 195 ARG 0.010 0.000 ARG P 510 *********************** 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 567 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 410 time to evaluate : 4.317 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: A 24 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7802 (pt) REVERT: A 74 MET cc_start: 0.7879 (tpt) cc_final: 0.7617 (tpt) REVERT: A 78 LEU cc_start: 0.8625 (tt) cc_final: 0.7958 (mm) REVERT: A 87 TRP cc_start: 0.8479 (t-100) cc_final: 0.8252 (t-100) REVERT: A 100 LEU cc_start: 0.7714 (mt) cc_final: 0.7460 (tt) REVERT: A 214 TYR cc_start: 0.9241 (t80) cc_final: 0.8773 (t80) REVERT: A 277 GLN cc_start: 0.8466 (pp30) cc_final: 0.8247 (pt0) REVERT: C 317 ARG cc_start: 0.8431 (mtt-85) cc_final: 0.8131 (mtm110) REVERT: C 319 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8642 (tt) REVERT: C 380 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 383 ASP cc_start: 0.8244 (m-30) cc_final: 0.8033 (m-30) REVERT: C 384 GLN cc_start: 0.8074 (tp-100) cc_final: 0.7525 (tp-100) REVERT: C 465 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7982 (mtm) REVERT: C 491 MET cc_start: 0.7974 (mmm) cc_final: 0.7689 (mmm) REVERT: D 317 ARG cc_start: 0.8507 (mtt-85) cc_final: 0.8196 (mtm110) REVERT: D 326 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8057 (mm-40) REVERT: D 380 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8381 (tm-30) REVERT: D 383 ASP cc_start: 0.8287 (m-30) cc_final: 0.8017 (m-30) REVERT: D 384 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7555 (tp-100) REVERT: D 440 MET cc_start: 0.8220 (ttp) cc_final: 0.7957 (ttp) REVERT: D 465 MET cc_start: 0.8267 (mtp) cc_final: 0.7655 (mtm) REVERT: D 491 MET cc_start: 0.8014 (mmm) cc_final: 0.7690 (mmm) REVERT: E 144 MET cc_start: 0.3749 (ttm) cc_final: 0.3439 (tpp) REVERT: E 239 GLU cc_start: 0.8747 (tp30) cc_final: 0.8479 (tp30) REVERT: E 289 ARG cc_start: 0.8610 (mmt-90) cc_final: 0.8232 (mpt180) REVERT: G 26 ARG cc_start: 0.7905 (mpt180) cc_final: 0.7565 (mmm160) REVERT: G 47 LYS cc_start: 0.8899 (ptpp) cc_final: 0.8693 (ptmt) REVERT: G 119 MET cc_start: 0.7993 (mpp) cc_final: 0.6873 (ttp) REVERT: G 163 ILE cc_start: 0.8709 (mm) cc_final: 0.8490 (mm) REVERT: G 288 TRP cc_start: 0.8733 (m100) cc_final: 0.8100 (m100) REVERT: G 294 ILE cc_start: 0.9176 (pt) cc_final: 0.8794 (mt) REVERT: I 6 PHE cc_start: 0.4872 (t80) cc_final: 0.4671 (t80) REVERT: I 174 PHE cc_start: 0.6666 (t80) cc_final: 0.6272 (t80) REVERT: I 197 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6614 (ttp) REVERT: I 201 TYR cc_start: 0.7504 (t80) cc_final: 0.7028 (t80) REVERT: I 399 ASN cc_start: 0.2266 (p0) cc_final: 0.1838 (p0) REVERT: J 6 PHE cc_start: 0.5552 (t80) cc_final: 0.5224 (t80) REVERT: J 197 MET cc_start: 0.6843 (ptm) cc_final: 0.6328 (ppp) REVERT: J 201 TYR cc_start: 0.7607 (t80) cc_final: 0.6852 (t80) REVERT: J 234 ARG cc_start: 0.8091 (mmm160) cc_final: 0.7542 (mmm160) REVERT: J 399 ASN cc_start: 0.2725 (p0) cc_final: 0.2269 (p0) REVERT: B 24 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7816 (pt) REVERT: B 71 ASP cc_start: 0.7665 (t0) cc_final: 0.7308 (t0) REVERT: B 78 LEU cc_start: 0.8623 (tt) cc_final: 0.7946 (mm) REVERT: H 26 ARG cc_start: 0.7880 (mpt180) cc_final: 0.7554 (mmm160) REVERT: H 47 LYS cc_start: 0.8960 (ptpp) cc_final: 0.8699 (ptmt) REVERT: H 163 ILE cc_start: 0.8754 (mm) cc_final: 0.8500 (mm) REVERT: H 274 TYR cc_start: 0.7131 (m-80) cc_final: 0.6535 (m-80) REVERT: H 288 TRP cc_start: 0.8755 (m100) cc_final: 0.8075 (m100) REVERT: H 294 ILE cc_start: 0.9196 (pt) cc_final: 0.8803 (mt) REVERT: F 144 MET cc_start: 0.3665 (ttm) cc_final: 0.3388 (tpp) REVERT: F 239 GLU cc_start: 0.8654 (tp30) cc_final: 0.8400 (tp30) REVERT: F 289 ARG cc_start: 0.8594 (mmt-90) cc_final: 0.8182 (mpt180) REVERT: K 170 LYS cc_start: 0.8274 (tppt) cc_final: 0.8057 (tppt) REVERT: K 195 TYR cc_start: 0.3292 (OUTLIER) cc_final: 0.3023 (p90) REVERT: O 192 VAL cc_start: 0.2411 (t) cc_final: 0.1974 (t) REVERT: O 201 MET cc_start: 0.3321 (mmm) cc_final: -0.0175 (ppp) REVERT: O 239 MET cc_start: 0.1633 (tpp) cc_final: -0.0538 (mtm) REVERT: O 257 GLU cc_start: 0.2741 (OUTLIER) cc_final: 0.1455 (pt0) REVERT: O 354 GLU cc_start: 0.1421 (OUTLIER) cc_final: -0.0167 (tt0) REVERT: O 428 THR cc_start: 0.1387 (OUTLIER) cc_final: 0.0596 (t) REVERT: L 120 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7335 (pp30) REVERT: L 195 TYR cc_start: 0.3897 (OUTLIER) cc_final: 0.3277 (p90) REVERT: P 354 GLU cc_start: 0.1386 (OUTLIER) cc_final: -0.0200 (tt0) REVERT: P 428 THR cc_start: 0.2476 (OUTLIER) cc_final: 0.1803 (t) REVERT: P 455 LYS cc_start: 0.4776 (mttm) cc_final: 0.4376 (mptt) outliers start: 157 outliers final: 77 residues processed: 542 average time/residue: 0.4816 time to fit residues: 434.3394 Evaluate side-chains 456 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 367 time to evaluate : 4.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 197 MET Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 381 ASP Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain K residue 195 TYR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 276 ASP Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 354 GLU Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 403 ASP Chi-restraints excluded: chain O residue 426 ILE Chi-restraints excluded: chain O residue 428 THR Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain O residue 476 VAL Chi-restraints excluded: chain L residue 8 PHE Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 195 TYR Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 426 ILE Chi-restraints excluded: chain P residue 428 THR Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 413 optimal weight: 0.5980 chunk 314 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 419 optimal weight: 10.0000 chunk 444 optimal weight: 30.0000 chunk 219 optimal weight: 9.9990 chunk 398 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS G 92 ASN J 215 GLN ** O 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 422 HIS P 450 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 37650 Z= 0.241 Angle : 0.675 14.295 50952 Z= 0.342 Chirality : 0.047 0.308 5958 Planarity : 0.004 0.053 6490 Dihedral : 6.606 73.087 5044 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.58 % Favored : 90.33 % Rotamer: Outliers : 3.91 % Allowed : 17.18 % Favored : 78.91 % 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: -2.60 (0.12), residues: 4604 helix: -0.83 (0.14), residues: 1410 sheet: -2.00 (0.19), residues: 660 loop : -2.22 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP K 132 HIS 0.005 0.001 HIS A 93 PHE 0.020 0.002 PHE I 223 TYR 0.022 0.002 TYR D 624 ARG 0.009 0.000 ARG I 234 *********************** 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 554 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 391 time to evaluate : 4.203 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: A 24 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7909 (pt) REVERT: A 71 ASP cc_start: 0.7695 (t0) cc_final: 0.7326 (t0) REVERT: A 74 MET cc_start: 0.7905 (tpt) cc_final: 0.7648 (tpt) REVERT: A 78 LEU cc_start: 0.8651 (tt) cc_final: 0.7992 (mm) REVERT: A 87 TRP cc_start: 0.8508 (t-100) cc_final: 0.8250 (t-100) REVERT: A 277 GLN cc_start: 0.8470 (pp30) cc_final: 0.8221 (pt0) REVERT: C 317 ARG cc_start: 0.8452 (mtt-85) cc_final: 0.7938 (mtm110) REVERT: C 319 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8685 (tt) REVERT: C 383 ASP cc_start: 0.8266 (m-30) cc_final: 0.8043 (m-30) REVERT: C 384 GLN cc_start: 0.8098 (tp-100) cc_final: 0.7567 (tp-100) REVERT: C 465 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8013 (mtm) REVERT: C 491 MET cc_start: 0.7921 (mmm) cc_final: 0.7564 (mmm) REVERT: D 296 MET cc_start: 0.8180 (tmm) cc_final: 0.7939 (tmm) REVERT: D 317 ARG cc_start: 0.8536 (mtt-85) cc_final: 0.8140 (ttm110) REVERT: D 326 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8015 (mm-40) REVERT: D 380 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8221 (tm-30) REVERT: D 383 ASP cc_start: 0.8321 (m-30) cc_final: 0.8074 (m-30) REVERT: D 384 GLN cc_start: 0.8110 (tp-100) cc_final: 0.7557 (tp-100) REVERT: D 465 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7651 (mtp) REVERT: D 491 MET cc_start: 0.7948 (mmm) cc_final: 0.7590 (mmm) REVERT: E 144 MET cc_start: 0.3718 (ttm) cc_final: 0.3423 (tpp) REVERT: E 239 GLU cc_start: 0.8763 (tp30) cc_final: 0.8517 (tp30) REVERT: E 289 ARG cc_start: 0.8610 (mmt-90) cc_final: 0.8204 (mpt180) REVERT: G 26 ARG cc_start: 0.7906 (mpt180) cc_final: 0.7553 (mmm160) REVERT: G 47 LYS cc_start: 0.8912 (ptpp) cc_final: 0.8633 (ptmt) REVERT: G 163 ILE cc_start: 0.8695 (mm) cc_final: 0.8493 (mm) REVERT: G 288 TRP cc_start: 0.8788 (m100) cc_final: 0.8037 (m100) REVERT: G 294 ILE cc_start: 0.9243 (pt) cc_final: 0.8859 (mt) REVERT: I 174 PHE cc_start: 0.6705 (t80) cc_final: 0.6309 (t80) REVERT: I 197 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6570 (ttp) REVERT: I 201 TYR cc_start: 0.7227 (t80) cc_final: 0.6759 (t80) REVERT: I 389 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7323 (tm-30) REVERT: I 399 ASN cc_start: 0.2196 (p0) cc_final: 0.1827 (p0) REVERT: J 6 PHE cc_start: 0.5626 (t80) cc_final: 0.5407 (t80) REVERT: J 201 TYR cc_start: 0.7233 (t80) cc_final: 0.6606 (t80) REVERT: J 234 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7504 (mmm160) REVERT: J 389 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7416 (tm-30) REVERT: J 399 ASN cc_start: 0.2716 (p0) cc_final: 0.2295 (p0) REVERT: B 71 ASP cc_start: 0.7730 (t0) cc_final: 0.7405 (t0) REVERT: B 78 LEU cc_start: 0.8726 (tt) cc_final: 0.8061 (mm) REVERT: B 101 PHE cc_start: 0.7940 (m-10) cc_final: 0.7615 (m-10) REVERT: B 204 SER cc_start: 0.8629 (m) cc_final: 0.8375 (p) REVERT: H 26 ARG cc_start: 0.7812 (mpt180) cc_final: 0.7496 (mmm160) REVERT: H 47 LYS cc_start: 0.8960 (ptpp) cc_final: 0.8716 (ptmt) REVERT: H 212 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7045 (mm-40) REVERT: H 288 TRP cc_start: 0.8829 (m100) cc_final: 0.8018 (m100) REVERT: H 294 ILE cc_start: 0.9207 (pt) cc_final: 0.8840 (mt) REVERT: F 121 MET cc_start: 0.8257 (tmm) cc_final: 0.7794 (tmm) REVERT: F 127 LYS cc_start: 0.5757 (tptt) cc_final: 0.5490 (tptp) REVERT: F 144 MET cc_start: 0.3675 (ttm) cc_final: 0.3411 (tpp) REVERT: F 289 ARG cc_start: 0.8623 (mmt-90) cc_final: 0.8223 (mpt180) REVERT: K 119 PHE cc_start: 0.6751 (t80) cc_final: 0.6470 (t80) REVERT: K 170 LYS cc_start: 0.8039 (tppt) cc_final: 0.7837 (tppt) REVERT: K 195 TYR cc_start: 0.3634 (OUTLIER) cc_final: 0.3011 (p90) REVERT: O 192 VAL cc_start: 0.1409 (t) cc_final: 0.0973 (t) REVERT: O 201 MET cc_start: 0.3392 (mmm) cc_final: -0.0191 (ppp) REVERT: O 239 MET cc_start: 0.1000 (tpp) cc_final: -0.0902 (mpp) REVERT: O 257 GLU cc_start: 0.2741 (OUTLIER) cc_final: 0.1679 (pt0) REVERT: O 428 THR cc_start: 0.1215 (OUTLIER) cc_final: 0.0398 (t) REVERT: L 45 MET cc_start: 0.7850 (tmm) cc_final: 0.7464 (ppp) REVERT: L 120 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7120 (pp30) REVERT: L 149 ILE cc_start: 0.2049 (OUTLIER) cc_final: 0.1816 (pt) REVERT: L 195 TYR cc_start: 0.2957 (OUTLIER) cc_final: 0.2574 (p90) REVERT: P 192 VAL cc_start: 0.1776 (t) cc_final: 0.1330 (t) REVERT: P 201 MET cc_start: 0.1653 (mmm) cc_final: -0.0510 (ttp) REVERT: P 354 GLU cc_start: 0.1949 (OUTLIER) cc_final: -0.0251 (tt0) REVERT: P 455 LYS cc_start: 0.4712 (mttm) cc_final: 0.4355 (mptt) outliers start: 163 outliers final: 98 residues processed: 525 average time/residue: 0.4763 time to fit residues: 417.9737 Evaluate side-chains 471 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 361 time to evaluate : 4.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 197 MET Chi-restraints excluded: chain I residue 281 SER Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 212 GLN Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 381 ASP Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain K residue 195 TYR Chi-restraints excluded: chain K residue 236 ASP Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 422 HIS Chi-restraints excluded: chain O residue 428 THR Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain O residue 449 LYS Chi-restraints excluded: chain O residue 463 MET Chi-restraints excluded: chain L residue 8 PHE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 195 TYR Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 370 optimal weight: 9.9990 chunk 252 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 331 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 379 optimal weight: 9.9990 chunk 307 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 chunk 399 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS H 92 ASN ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 228 GLN ** O 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 221 ASN ** P 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 37650 Z= 0.243 Angle : 0.662 13.236 50952 Z= 0.335 Chirality : 0.046 0.279 5958 Planarity : 0.004 0.082 6490 Dihedral : 6.304 71.233 5041 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.73 % Favored : 90.18 % Rotamer: Outliers : 4.15 % Allowed : 17.95 % Favored : 77.90 % 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: -2.46 (0.12), residues: 4604 helix: -0.68 (0.14), residues: 1412 sheet: -1.96 (0.19), residues: 676 loop : -2.13 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP K 132 HIS 0.006 0.001 HIS B 93 PHE 0.025 0.002 PHE J 174 TYR 0.017 0.002 TYR K 195 ARG 0.014 0.000 ARG I 234 *********************** 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 559 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 386 time to evaluate : 3.956 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: A 71 ASP cc_start: 0.7823 (t0) cc_final: 0.7422 (t0) REVERT: A 74 MET cc_start: 0.7935 (tpt) cc_final: 0.7343 (tpt) REVERT: A 78 LEU cc_start: 0.8643 (tt) cc_final: 0.7960 (mm) REVERT: A 87 TRP cc_start: 0.8537 (t-100) cc_final: 0.8294 (t-100) REVERT: A 283 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8516 (pp) REVERT: C 319 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8450 (tt) REVERT: C 325 HIS cc_start: 0.7422 (t-90) cc_final: 0.6948 (t70) REVERT: C 384 GLN cc_start: 0.8151 (tp-100) cc_final: 0.7152 (tp-100) REVERT: C 388 ASP cc_start: 0.8157 (m-30) cc_final: 0.7642 (m-30) REVERT: C 465 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7930 (mtm) REVERT: C 491 MET cc_start: 0.7915 (mmm) cc_final: 0.7560 (mmm) REVERT: D 326 GLN cc_start: 0.8554 (mm-40) cc_final: 0.7937 (mm-40) REVERT: D 380 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8201 (tm-30) REVERT: D 383 ASP cc_start: 0.8252 (m-30) cc_final: 0.8049 (m-30) REVERT: D 384 GLN cc_start: 0.8125 (tp-100) cc_final: 0.7172 (tp-100) REVERT: D 388 ASP cc_start: 0.8154 (m-30) cc_final: 0.7641 (m-30) REVERT: D 465 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7656 (mtp) REVERT: D 491 MET cc_start: 0.7934 (mmm) cc_final: 0.7586 (mmm) REVERT: E 23 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8114 (t0) REVERT: E 121 MET cc_start: 0.8212 (tmm) cc_final: 0.7686 (tmm) REVERT: E 144 MET cc_start: 0.3724 (ttm) cc_final: 0.3459 (tpp) REVERT: E 239 GLU cc_start: 0.8822 (tp30) cc_final: 0.8587 (tp30) REVERT: E 289 ARG cc_start: 0.8590 (mmt-90) cc_final: 0.8138 (mpt180) REVERT: G 26 ARG cc_start: 0.7867 (mpt180) cc_final: 0.7562 (mmm160) REVERT: G 47 LYS cc_start: 0.8977 (ptpp) cc_final: 0.8755 (ptmt) REVERT: G 119 MET cc_start: 0.8128 (mpp) cc_final: 0.6801 (ttp) REVERT: G 128 ILE cc_start: 0.8362 (mm) cc_final: 0.8137 (mm) REVERT: G 163 ILE cc_start: 0.8536 (mm) cc_final: 0.8297 (mm) REVERT: G 288 TRP cc_start: 0.8837 (m100) cc_final: 0.7960 (m100) REVERT: G 294 ILE cc_start: 0.9245 (pt) cc_final: 0.8878 (mt) REVERT: I 174 PHE cc_start: 0.6755 (t80) cc_final: 0.6369 (t80) REVERT: I 197 MET cc_start: 0.7177 (ttt) cc_final: 0.6439 (ttp) REVERT: I 201 TYR cc_start: 0.7197 (t80) cc_final: 0.6750 (t80) REVERT: I 399 ASN cc_start: 0.2943 (p0) cc_final: 0.2623 (p0) REVERT: J 201 TYR cc_start: 0.7228 (t80) cc_final: 0.6666 (t80) REVERT: J 399 ASN cc_start: 0.3071 (p0) cc_final: 0.2622 (p0) REVERT: B 71 ASP cc_start: 0.7783 (t0) cc_final: 0.7380 (t0) REVERT: B 78 LEU cc_start: 0.8711 (tt) cc_final: 0.8074 (mm) REVERT: B 87 TRP cc_start: 0.8404 (t-100) cc_final: 0.8154 (t-100) REVERT: B 101 PHE cc_start: 0.7921 (m-10) cc_final: 0.7604 (m-10) REVERT: H 26 ARG cc_start: 0.7819 (mpt180) cc_final: 0.7502 (mmm160) REVERT: H 47 LYS cc_start: 0.8945 (ptpp) cc_final: 0.8695 (ptmt) REVERT: H 211 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8220 (mm) REVERT: H 294 ILE cc_start: 0.9241 (pt) cc_final: 0.8868 (mt) REVERT: F 23 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7957 (t0) REVERT: F 144 MET cc_start: 0.3689 (ttm) cc_final: 0.3385 (tpp) REVERT: F 289 ARG cc_start: 0.8607 (mmt-90) cc_final: 0.8158 (mpt180) REVERT: K 120 GLN cc_start: 0.7145 (mp10) cc_final: 0.6591 (pp30) REVERT: K 195 TYR cc_start: 0.3294 (OUTLIER) cc_final: 0.2967 (p90) REVERT: O 192 VAL cc_start: 0.1653 (t) cc_final: 0.1142 (t) REVERT: O 201 MET cc_start: 0.3354 (mmm) cc_final: -0.0625 (ppp) REVERT: O 239 MET cc_start: 0.0344 (tpp) cc_final: -0.1083 (mpp) REVERT: O 257 GLU cc_start: 0.2986 (mp0) cc_final: 0.1264 (pt0) REVERT: L 120 GLN cc_start: 0.8111 (mm-40) cc_final: 0.6926 (pp30) REVERT: L 195 TYR cc_start: 0.3883 (OUTLIER) cc_final: 0.3675 (p90) REVERT: P 192 VAL cc_start: 0.1531 (t) cc_final: 0.1070 (t) REVERT: P 354 GLU cc_start: 0.2453 (OUTLIER) cc_final: 0.0212 (tt0) REVERT: P 455 LYS cc_start: 0.4681 (mttm) cc_final: 0.4339 (mptt) outliers start: 173 outliers final: 122 residues processed: 523 average time/residue: 0.4735 time to fit residues: 414.8327 Evaluate side-chains 491 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 359 time to evaluate : 4.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 281 SER Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 381 ASP Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain K residue 195 TYR Chi-restraints excluded: chain K residue 236 ASP Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 276 ASP Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 373 ILE Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 422 HIS Chi-restraints excluded: chain O residue 426 ILE Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain O residue 449 LYS Chi-restraints excluded: chain L residue 8 PHE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 195 TYR Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 373 ILE Chi-restraints excluded: chain P residue 400 THR Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 149 optimal weight: 10.0000 chunk 400 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 445 optimal weight: 20.0000 chunk 369 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 HIS ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 508 HIS ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37650 Z= 0.263 Angle : 0.670 13.777 50952 Z= 0.339 Chirality : 0.047 0.236 5958 Planarity : 0.004 0.062 6490 Dihedral : 6.113 70.352 5036 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.90 % Favored : 90.01 % Rotamer: Outliers : 4.51 % Allowed : 18.47 % Favored : 77.02 % 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: -2.40 (0.12), residues: 4604 helix: -0.58 (0.14), residues: 1398 sheet: -1.93 (0.19), residues: 678 loop : -2.12 (0.13), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 132 HIS 0.006 0.001 HIS A 93 PHE 0.016 0.002 PHE J 223 TYR 0.018 0.002 TYR K 195 ARG 0.015 0.001 ARG I 234 *********************** REFINEMENT MACRO_CYCLE 6 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 568 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 380 time to evaluate : 4.570 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: A 71 ASP cc_start: 0.7844 (t0) cc_final: 0.7510 (t0) REVERT: A 74 MET cc_start: 0.7883 (tpt) cc_final: 0.7634 (tpt) REVERT: A 78 LEU cc_start: 0.8634 (tt) cc_final: 0.7993 (mm) REVERT: A 87 TRP cc_start: 0.8558 (t-100) cc_final: 0.8319 (t-100) REVERT: A 101 PHE cc_start: 0.8120 (m-10) cc_final: 0.7755 (m-10) REVERT: A 233 SER cc_start: 0.9045 (m) cc_final: 0.8802 (m) REVERT: A 249 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7315 (ppp) REVERT: C 296 MET cc_start: 0.8166 (tmm) cc_final: 0.7958 (tmm) REVERT: C 319 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8424 (tt) REVERT: C 384 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7306 (tp-100) REVERT: C 388 ASP cc_start: 0.8186 (m-30) cc_final: 0.7744 (m-30) REVERT: C 465 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8362 (mtm) REVERT: D 296 MET cc_start: 0.8176 (tmm) cc_final: 0.7976 (tmm) REVERT: D 326 GLN cc_start: 0.8544 (mm-40) cc_final: 0.7928 (mm-40) REVERT: D 383 ASP cc_start: 0.8282 (m-30) cc_final: 0.8070 (m-30) REVERT: D 384 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7222 (tp-100) REVERT: D 388 ASP cc_start: 0.8172 (m-30) cc_final: 0.7680 (m-30) REVERT: D 465 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7745 (mtp) REVERT: E 121 MET cc_start: 0.8282 (tmm) cc_final: 0.7767 (tmm) REVERT: E 144 MET cc_start: 0.3728 (ttm) cc_final: 0.3176 (tpp) REVERT: E 289 ARG cc_start: 0.8581 (mmt-90) cc_final: 0.8139 (mpt180) REVERT: G 26 ARG cc_start: 0.7870 (mpt180) cc_final: 0.7511 (mmm160) REVERT: G 47 LYS cc_start: 0.8925 (ptpp) cc_final: 0.8697 (ptmt) REVERT: G 119 MET cc_start: 0.8297 (mpp) cc_final: 0.7217 (ttp) REVERT: G 150 GLU cc_start: 0.8788 (mp0) cc_final: 0.8544 (mp0) REVERT: G 163 ILE cc_start: 0.8545 (mm) cc_final: 0.8237 (mm) REVERT: G 294 ILE cc_start: 0.9253 (pt) cc_final: 0.8904 (mt) REVERT: I 174 PHE cc_start: 0.6785 (t80) cc_final: 0.6416 (t80) REVERT: I 197 MET cc_start: 0.7137 (ttt) cc_final: 0.6406 (ttp) REVERT: I 201 TYR cc_start: 0.7270 (t80) cc_final: 0.6902 (t80) REVERT: I 389 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7424 (tm-30) REVERT: I 399 ASN cc_start: 0.2779 (p0) cc_final: 0.2492 (p0) REVERT: J 76 MET cc_start: 0.6049 (pmm) cc_final: 0.4725 (mtm) REVERT: J 201 TYR cc_start: 0.7283 (t80) cc_final: 0.6819 (t80) REVERT: J 389 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7408 (tm-30) REVERT: J 399 ASN cc_start: 0.2963 (p0) cc_final: 0.2727 (p0) REVERT: B 71 ASP cc_start: 0.7786 (t0) cc_final: 0.7526 (t0) REVERT: B 74 MET cc_start: 0.7823 (tpt) cc_final: 0.7436 (tpt) REVERT: B 78 LEU cc_start: 0.8717 (tt) cc_final: 0.8114 (mm) REVERT: B 101 PHE cc_start: 0.7966 (m-10) cc_final: 0.7629 (m-10) REVERT: B 233 SER cc_start: 0.8944 (m) cc_final: 0.8675 (m) REVERT: B 249 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7449 (ppp) REVERT: B 283 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8379 (pp) REVERT: B 285 THR cc_start: 0.8078 (p) cc_final: 0.7855 (p) REVERT: H 26 ARG cc_start: 0.7843 (mpt180) cc_final: 0.7507 (mmm160) REVERT: H 47 LYS cc_start: 0.8900 (ptpp) cc_final: 0.8687 (ptmt) REVERT: H 211 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8220 (mm) REVERT: H 294 ILE cc_start: 0.9250 (pt) cc_final: 0.8898 (mt) REVERT: F 121 MET cc_start: 0.8214 (tmm) cc_final: 0.7935 (tmm) REVERT: F 127 LYS cc_start: 0.5986 (tptt) cc_final: 0.5579 (tptp) REVERT: F 144 MET cc_start: 0.3691 (ttm) cc_final: 0.3387 (tpp) REVERT: F 289 ARG cc_start: 0.8578 (mmt-90) cc_final: 0.8117 (mpt180) REVERT: K 119 PHE cc_start: 0.6702 (t80) cc_final: 0.6488 (t80) REVERT: K 120 GLN cc_start: 0.7285 (mp10) cc_final: 0.6694 (pp30) REVERT: K 195 TYR cc_start: 0.3287 (OUTLIER) cc_final: 0.3056 (p90) REVERT: O 192 VAL cc_start: 0.1041 (t) cc_final: 0.0639 (t) REVERT: O 201 MET cc_start: 0.2826 (mmm) cc_final: -0.0746 (ppp) REVERT: O 239 MET cc_start: 0.0117 (tpp) cc_final: -0.1038 (mpp) REVERT: O 254 MET cc_start: 0.0942 (mpp) cc_final: 0.0636 (mpp) REVERT: L 120 GLN cc_start: 0.8173 (mm-40) cc_final: 0.6891 (pp30) REVERT: L 170 LYS cc_start: 0.8099 (tppt) cc_final: 0.7776 (tptp) REVERT: P 201 MET cc_start: 0.1595 (mmm) cc_final: -0.0934 (ttp) REVERT: P 455 LYS cc_start: 0.4580 (mttm) cc_final: 0.4191 (mptt) outliers start: 188 outliers final: 135 residues processed: 525 average time/residue: 0.4639 time to fit residues: 410.0796 Evaluate side-chains 507 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 364 time to evaluate : 4.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 281 SER Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 381 ASP Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 195 TYR Chi-restraints excluded: chain K residue 236 ASP Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 276 ASP Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 373 ILE Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 422 HIS Chi-restraints excluded: chain O residue 426 ILE Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain L residue 8 PHE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 138 PHE Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 373 ILE Chi-restraints excluded: chain P residue 400 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 429 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 253 optimal weight: 0.2980 chunk 325 optimal weight: 5.9990 chunk 251 optimal weight: 0.0370 chunk 374 optimal weight: 30.0000 chunk 248 optimal weight: 0.8980 chunk 443 optimal weight: 6.9990 chunk 277 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN J 156 GLN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN O 221 ASN ** O 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 151 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.3812 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 : 0.632 13.714 50952 Z= 0.318 Chirality : 0.045 0.287 5958 Planarity : 0.004 0.055 6490 Dihedral : 5.778 68.872 5033 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.47 % Favored : 91.44 % Rotamer: Outliers : 3.38 % Allowed : 20.08 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.12), residues: 4604 helix: -0.37 (0.14), residues: 1394 sheet: -1.78 (0.19), residues: 676 loop : -1.96 (0.13), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP L 132 HIS 0.006 0.001 HIS C 325 PHE 0.044 0.001 PHE B 73 TYR 0.018 0.001 TYR K 195 ARG 0.011 0.000 ARG I 234 *********************** REFINEMENT MACRO_CYCLE 7 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 545 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 404 time to evaluate : 4.379 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: A 71 ASP cc_start: 0.7521 (t0) cc_final: 0.7210 (t0) REVERT: A 74 MET cc_start: 0.7865 (tpt) cc_final: 0.7359 (tpt) REVERT: A 78 LEU cc_start: 0.8597 (tt) cc_final: 0.7926 (mm) REVERT: A 101 PHE cc_start: 0.8032 (m-10) cc_final: 0.7632 (m-10) REVERT: A 233 SER cc_start: 0.8861 (m) cc_final: 0.8607 (m) REVERT: A 235 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8430 (mttt) REVERT: C 319 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8389 (tt) REVERT: C 384 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7317 (tp-100) REVERT: C 388 ASP cc_start: 0.8185 (m-30) cc_final: 0.7752 (m-30) REVERT: C 465 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8246 (mtm) REVERT: C 491 MET cc_start: 0.7893 (mmm) cc_final: 0.7693 (mmm) REVERT: C 498 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7282 (ttt90) REVERT: D 296 MET cc_start: 0.8152 (tmm) cc_final: 0.7946 (tmm) REVERT: D 317 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.7971 (mtm110) REVERT: D 326 GLN cc_start: 0.8552 (mm-40) cc_final: 0.7932 (mm-40) REVERT: D 383 ASP cc_start: 0.8188 (m-30) cc_final: 0.7966 (m-30) REVERT: D 384 GLN cc_start: 0.8176 (tp-100) cc_final: 0.7204 (tp-100) REVERT: D 388 ASP cc_start: 0.8177 (m-30) cc_final: 0.7657 (m-30) REVERT: D 465 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7944 (mtm) REVERT: D 491 MET cc_start: 0.7937 (mmm) cc_final: 0.7649 (mmm) REVERT: E 121 MET cc_start: 0.8199 (tmm) cc_final: 0.7703 (tmm) REVERT: E 144 MET cc_start: 0.3657 (ttm) cc_final: 0.3232 (tpp) REVERT: E 289 ARG cc_start: 0.8529 (mmt-90) cc_final: 0.8053 (mpt180) REVERT: G 26 ARG cc_start: 0.7934 (mpt180) cc_final: 0.7617 (mmm160) REVERT: G 47 LYS cc_start: 0.8899 (ptpp) cc_final: 0.8672 (ptmt) REVERT: G 119 MET cc_start: 0.8174 (mpp) cc_final: 0.7215 (ttp) REVERT: G 150 GLU cc_start: 0.8818 (mp0) cc_final: 0.8596 (mp0) REVERT: G 163 ILE cc_start: 0.8512 (mm) cc_final: 0.8206 (mm) REVERT: G 211 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8037 (mm) REVERT: G 294 ILE cc_start: 0.9231 (pt) cc_final: 0.8871 (mt) REVERT: I 174 PHE cc_start: 0.6752 (t80) cc_final: 0.6354 (t80) REVERT: I 201 TYR cc_start: 0.7147 (t80) cc_final: 0.6795 (t80) REVERT: I 389 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7385 (tm-30) REVERT: J 201 TYR cc_start: 0.7168 (t80) cc_final: 0.6729 (t80) REVERT: J 389 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7555 (tm-30) REVERT: B 71 ASP cc_start: 0.7634 (t0) cc_final: 0.7221 (t0) REVERT: B 78 LEU cc_start: 0.8624 (tt) cc_final: 0.7963 (mm) REVERT: B 87 TRP cc_start: 0.8369 (t-100) cc_final: 0.8156 (t-100) REVERT: B 101 PHE cc_start: 0.7940 (m-10) cc_final: 0.7503 (m-10) REVERT: B 233 SER cc_start: 0.8756 (m) cc_final: 0.8493 (m) REVERT: B 235 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8359 (mttt) REVERT: H 26 ARG cc_start: 0.7892 (mpt180) cc_final: 0.7558 (mmm160) REVERT: H 47 LYS cc_start: 0.8924 (ptpp) cc_final: 0.8691 (ptmt) REVERT: H 212 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.6944 (tm-30) REVERT: H 294 ILE cc_start: 0.9234 (pt) cc_final: 0.8862 (mt) REVERT: F 289 ARG cc_start: 0.8539 (mmt-90) cc_final: 0.8054 (mpt180) REVERT: O 192 VAL cc_start: 0.0953 (t) cc_final: 0.0614 (t) REVERT: O 201 MET cc_start: 0.2806 (mmm) cc_final: -0.0850 (ppp) REVERT: O 239 MET cc_start: 0.0191 (tpp) cc_final: -0.0952 (mpp) REVERT: O 254 MET cc_start: 0.1519 (mpp) cc_final: 0.1276 (mpp) REVERT: O 332 ASP cc_start: 0.2302 (m-30) cc_final: 0.1494 (t70) REVERT: L 45 MET cc_start: 0.8371 (tmm) cc_final: 0.8074 (ppp) REVERT: L 103 GLN cc_start: 0.9290 (tp-100) cc_final: 0.9087 (tp-100) REVERT: L 120 GLN cc_start: 0.8114 (mm-40) cc_final: 0.6866 (pp30) REVERT: L 170 LYS cc_start: 0.8101 (tppt) cc_final: 0.7777 (tptp) REVERT: P 201 MET cc_start: 0.1441 (mmm) cc_final: -0.0976 (ttp) REVERT: P 455 LYS cc_start: 0.4503 (mttm) cc_final: 0.4148 (mptt) outliers start: 141 outliers final: 89 residues processed: 513 average time/residue: 0.4687 time to fit residues: 401.6919 Evaluate side-chains 475 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 381 time to evaluate : 4.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 212 GLN Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 351 ILE Chi-restraints excluded: chain H residue 381 ASP Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain K residue 236 ASP Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 422 HIS Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain O residue 449 LYS Chi-restraints excluded: chain L residue 8 PHE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 400 THR Chi-restraints excluded: chain P residue 443 VAL Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 274 optimal weight: 5.9990 chunk 177 optimal weight: 0.3980 chunk 264 optimal weight: 6.9990 chunk 133 optimal weight: 0.0030 chunk 87 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 281 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 348 optimal weight: 1.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 HIS ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37650 Z= 0.171 Angle : 0.640 14.310 50952 Z= 0.318 Chirality : 0.045 0.235 5958 Planarity : 0.004 0.055 6490 Dihedral : 5.595 67.106 5033 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.49 % Favored : 91.42 % Rotamer: Outliers : 3.21 % Allowed : 20.47 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.13), residues: 4604 helix: -0.23 (0.14), residues: 1372 sheet: -1.71 (0.19), residues: 668 loop : -1.93 (0.13), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP L 132 HIS 0.006 0.001 HIS D 325 PHE 0.038 0.001 PHE J 174 TYR 0.033 0.001 TYR B 304 ARG 0.009 0.000 ARG I 234 *********************** REFINEMENT MACRO_CYCLE 8 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 543 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 409 time to evaluate : 4.308 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: A 20 MET cc_start: 0.6997 (pmm) cc_final: 0.6637 (pmm) REVERT: A 71 ASP cc_start: 0.7737 (t0) cc_final: 0.7431 (t0) REVERT: A 74 MET cc_start: 0.7796 (tpt) cc_final: 0.7141 (tpt) REVERT: A 78 LEU cc_start: 0.8682 (tt) cc_final: 0.8032 (mm) REVERT: A 87 TRP cc_start: 0.8593 (t-100) cc_final: 0.8311 (t60) REVERT: A 101 PHE cc_start: 0.8053 (m-10) cc_final: 0.7618 (m-10) REVERT: A 233 SER cc_start: 0.8765 (m) cc_final: 0.8564 (m) REVERT: A 235 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8423 (mttt) REVERT: C 274 ILE cc_start: 0.9203 (mt) cc_final: 0.8760 (tt) REVERT: C 317 ARG cc_start: 0.8453 (mtt-85) cc_final: 0.7966 (mtm110) REVERT: C 319 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8432 (tt) REVERT: C 384 GLN cc_start: 0.8302 (tp-100) cc_final: 0.7421 (tp-100) REVERT: C 388 ASP cc_start: 0.8248 (m-30) cc_final: 0.7926 (m-30) REVERT: C 465 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8167 (mtm) REVERT: C 491 MET cc_start: 0.7897 (mmm) cc_final: 0.7662 (mmm) REVERT: C 498 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7252 (ttt90) REVERT: D 317 ARG cc_start: 0.8453 (mtt-85) cc_final: 0.7949 (mtm110) REVERT: D 326 GLN cc_start: 0.8501 (mm-40) cc_final: 0.7951 (mm-40) REVERT: D 383 ASP cc_start: 0.8162 (m-30) cc_final: 0.7919 (m-30) REVERT: D 384 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7240 (tp-100) REVERT: D 388 ASP cc_start: 0.8184 (m-30) cc_final: 0.7677 (m-30) REVERT: D 465 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7557 (mtp) REVERT: D 491 MET cc_start: 0.7899 (mmm) cc_final: 0.7678 (mmm) REVERT: D 498 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7304 (ttt90) REVERT: E 144 MET cc_start: 0.3822 (ttm) cc_final: 0.3499 (tpp) REVERT: E 289 ARG cc_start: 0.8525 (mmt-90) cc_final: 0.8078 (mpt180) REVERT: G 26 ARG cc_start: 0.7895 (mpt180) cc_final: 0.7609 (mmm160) REVERT: G 47 LYS cc_start: 0.8879 (ptpp) cc_final: 0.8650 (ptmt) REVERT: G 119 MET cc_start: 0.8198 (mpp) cc_final: 0.7265 (ttp) REVERT: G 128 ILE cc_start: 0.8544 (mm) cc_final: 0.8273 (mm) REVERT: G 150 GLU cc_start: 0.8793 (mp0) cc_final: 0.8560 (mp0) REVERT: G 163 ILE cc_start: 0.8513 (mm) cc_final: 0.8173 (mm) REVERT: G 211 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8011 (mm) REVERT: G 294 ILE cc_start: 0.9226 (pt) cc_final: 0.8886 (mt) REVERT: I 174 PHE cc_start: 0.6725 (t80) cc_final: 0.6358 (t80) REVERT: I 188 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7814 (mmm160) REVERT: I 201 TYR cc_start: 0.7129 (t80) cc_final: 0.6697 (t80) REVERT: I 252 TYR cc_start: 0.6209 (m-80) cc_final: 0.5705 (m-80) REVERT: I 389 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7389 (tm-30) REVERT: J 201 TYR cc_start: 0.7124 (t80) cc_final: 0.6653 (t80) REVERT: J 389 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7515 (tm-30) REVERT: B 71 ASP cc_start: 0.7530 (t0) cc_final: 0.7234 (t0) REVERT: B 78 LEU cc_start: 0.8636 (tt) cc_final: 0.7987 (mm) REVERT: B 101 PHE cc_start: 0.7937 (m-10) cc_final: 0.7640 (m-10) REVERT: B 233 SER cc_start: 0.8700 (m) cc_final: 0.8388 (m) REVERT: B 235 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8464 (mttt) REVERT: H 26 ARG cc_start: 0.7860 (mpt180) cc_final: 0.7495 (mmm160) REVERT: H 47 LYS cc_start: 0.8903 (ptpp) cc_final: 0.8673 (ptmt) REVERT: H 212 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6902 (tp40) REVERT: H 294 ILE cc_start: 0.9233 (pt) cc_final: 0.8885 (mt) REVERT: F 144 MET cc_start: 0.4463 (tpp) cc_final: 0.3153 (tpp) REVERT: F 289 ARG cc_start: 0.8546 (mmt-90) cc_final: 0.8100 (mpt180) REVERT: K 120 GLN cc_start: 0.7335 (mp10) cc_final: 0.6622 (pp30) REVERT: O 192 VAL cc_start: 0.0952 (t) cc_final: 0.0593 (t) REVERT: O 201 MET cc_start: 0.3024 (mmm) cc_final: -0.0699 (ppp) REVERT: O 239 MET cc_start: 0.0065 (tpp) cc_final: -0.0951 (mpp) REVERT: O 254 MET cc_start: 0.1533 (mpp) cc_final: 0.1314 (mpp) REVERT: O 332 ASP cc_start: 0.2271 (m-30) cc_final: 0.1506 (t70) REVERT: L 45 MET cc_start: 0.8467 (tmm) cc_final: 0.8191 (ppp) REVERT: L 120 GLN cc_start: 0.8203 (mm-40) cc_final: 0.6989 (pp30) REVERT: L 170 LYS cc_start: 0.8120 (tppt) cc_final: 0.7791 (tptp) REVERT: P 184 LYS cc_start: 0.4042 (mmtt) cc_final: 0.2372 (tmtt) REVERT: P 201 MET cc_start: 0.1564 (mmm) cc_final: -0.0801 (ttp) REVERT: P 455 LYS cc_start: 0.4468 (mttm) cc_final: 0.4126 (mptt) REVERT: P 502 SER cc_start: 0.1906 (OUTLIER) cc_final: 0.1311 (t) outliers start: 134 outliers final: 88 residues processed: 508 average time/residue: 0.5144 time to fit residues: 441.2766 Evaluate side-chains 468 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 374 time to evaluate : 4.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 212 GLN Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 351 ILE Chi-restraints excluded: chain H residue 381 ASP Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain K residue 236 ASP Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 422 HIS Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain L residue 8 PHE Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 400 THR Chi-restraints excluded: chain P residue 443 VAL Chi-restraints excluded: chain P residue 463 MET Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 403 optimal weight: 0.9990 chunk 424 optimal weight: 7.9990 chunk 387 optimal weight: 9.9990 chunk 413 optimal weight: 5.9990 chunk 248 optimal weight: 0.0970 chunk 179 optimal weight: 30.0000 chunk 324 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 373 optimal weight: 0.4980 chunk 390 optimal weight: 0.8980 chunk 411 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 HIS ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN ** O 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 GLN P 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37650 Z= 0.168 Angle : 0.641 12.840 50952 Z= 0.317 Chirality : 0.045 0.214 5958 Planarity : 0.004 0.056 6490 Dihedral : 5.456 65.186 5033 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.95 % Favored : 91.96 % Rotamer: Outliers : 2.98 % Allowed : 21.02 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.13), residues: 4604 helix: -0.14 (0.14), residues: 1358 sheet: -1.64 (0.20), residues: 654 loop : -1.87 (0.13), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 87 HIS 0.007 0.001 HIS D 325 PHE 0.023 0.001 PHE J 174 TYR 0.024 0.001 TYR B 304 ARG 0.009 0.000 ARG I 234 *********************** REFINEMENT MACRO_CYCLE 9 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 515 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 391 time to evaluate : 4.368 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: A 20 MET cc_start: 0.6943 (pmm) cc_final: 0.6574 (pmm) REVERT: A 71 ASP cc_start: 0.7741 (t0) cc_final: 0.7418 (t0) REVERT: A 74 MET cc_start: 0.7751 (tpt) cc_final: 0.7124 (tpt) REVERT: A 78 LEU cc_start: 0.8696 (tt) cc_final: 0.8047 (mm) REVERT: A 99 GLN cc_start: 0.8624 (pm20) cc_final: 0.8201 (pm20) REVERT: A 101 PHE cc_start: 0.8019 (m-10) cc_final: 0.7694 (m-10) REVERT: A 233 SER cc_start: 0.8717 (m) cc_final: 0.8462 (m) REVERT: A 235 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8530 (mttt) REVERT: C 274 ILE cc_start: 0.9209 (mt) cc_final: 0.8790 (tt) REVERT: C 280 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7653 (m170) REVERT: C 317 ARG cc_start: 0.8444 (mtt-85) cc_final: 0.7944 (mtm110) REVERT: C 319 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8579 (tm) REVERT: C 368 CYS cc_start: 0.8883 (t) cc_final: 0.8434 (m) REVERT: C 384 GLN cc_start: 0.8358 (tp-100) cc_final: 0.7516 (tp-100) REVERT: C 388 ASP cc_start: 0.8269 (m-30) cc_final: 0.8018 (m-30) REVERT: C 465 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7641 (mtp) REVERT: C 491 MET cc_start: 0.7894 (mmm) cc_final: 0.7639 (mmm) REVERT: D 280 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7538 (m170) REVERT: D 317 ARG cc_start: 0.8435 (mtt-85) cc_final: 0.7933 (mtm110) REVERT: D 326 GLN cc_start: 0.8481 (mm-40) cc_final: 0.7935 (mm-40) REVERT: D 368 CYS cc_start: 0.8908 (t) cc_final: 0.8508 (m) REVERT: D 383 ASP cc_start: 0.8069 (m-30) cc_final: 0.7867 (m-30) REVERT: D 384 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7280 (tp-100) REVERT: D 388 ASP cc_start: 0.8192 (m-30) cc_final: 0.7692 (m-30) REVERT: D 465 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7804 (mtm) REVERT: D 491 MET cc_start: 0.7923 (mmm) cc_final: 0.7703 (mmm) REVERT: D 498 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7317 (ttt90) REVERT: E 121 MET cc_start: 0.7974 (tmm) cc_final: 0.7765 (tmm) REVERT: E 144 MET cc_start: 0.3814 (ttm) cc_final: 0.3499 (tpp) REVERT: G 26 ARG cc_start: 0.7891 (mpt180) cc_final: 0.7546 (mmm160) REVERT: G 47 LYS cc_start: 0.8908 (ptpp) cc_final: 0.8699 (ptmt) REVERT: G 119 MET cc_start: 0.8288 (mpp) cc_final: 0.7419 (ttp) REVERT: G 163 ILE cc_start: 0.8497 (mm) cc_final: 0.8192 (mm) REVERT: G 211 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7990 (mm) REVERT: G 294 ILE cc_start: 0.9224 (pt) cc_final: 0.8886 (mt) REVERT: I 174 PHE cc_start: 0.6714 (t80) cc_final: 0.6362 (t80) REVERT: I 188 ARG cc_start: 0.7939 (mmm160) cc_final: 0.7732 (mmm160) REVERT: I 201 TYR cc_start: 0.7083 (t80) cc_final: 0.6679 (t80) REVERT: I 389 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7580 (tm-30) REVERT: J 115 ARG cc_start: 0.2724 (tpp-160) cc_final: 0.2476 (tpp-160) REVERT: J 197 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6412 (ttp) REVERT: J 201 TYR cc_start: 0.7049 (t80) cc_final: 0.6560 (t80) REVERT: J 389 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7500 (tm-30) REVERT: B 71 ASP cc_start: 0.7679 (t0) cc_final: 0.7390 (t0) REVERT: B 78 LEU cc_start: 0.8630 (tt) cc_final: 0.7969 (mm) REVERT: B 101 PHE cc_start: 0.7933 (m-10) cc_final: 0.7635 (m-10) REVERT: B 233 SER cc_start: 0.8637 (m) cc_final: 0.8384 (m) REVERT: B 235 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8475 (mttt) REVERT: H 26 ARG cc_start: 0.7857 (mpt180) cc_final: 0.7548 (mmm160) REVERT: H 212 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: H 294 ILE cc_start: 0.9231 (pt) cc_final: 0.8884 (mt) REVERT: F 127 LYS cc_start: 0.5995 (tptt) cc_final: 0.5756 (tppt) REVERT: F 144 MET cc_start: 0.4189 (tpp) cc_final: 0.3237 (tpp) REVERT: F 289 ARG cc_start: 0.8529 (mmt-90) cc_final: 0.8066 (mpt180) REVERT: K 120 GLN cc_start: 0.7451 (mp10) cc_final: 0.6640 (pp30) REVERT: O 192 VAL cc_start: 0.0910 (t) cc_final: 0.0582 (t) REVERT: O 201 MET cc_start: 0.2837 (mmm) cc_final: 0.2493 (mmt) REVERT: O 239 MET cc_start: 0.0172 (tpp) cc_final: -0.0673 (mpp) REVERT: O 254 MET cc_start: 0.1430 (mpp) cc_final: 0.0824 (mpp) REVERT: O 332 ASP cc_start: 0.2262 (m-30) cc_final: 0.1517 (t70) REVERT: L 45 MET cc_start: 0.8641 (tmm) cc_final: 0.8417 (ppp) REVERT: L 120 GLN cc_start: 0.8190 (mm-40) cc_final: 0.6979 (pp30) REVERT: L 170 LYS cc_start: 0.8142 (tppt) cc_final: 0.7800 (tptp) REVERT: P 184 LYS cc_start: 0.4114 (mmtt) cc_final: 0.2486 (tmtt) REVERT: P 201 MET cc_start: 0.1520 (mmm) cc_final: -0.0774 (ttp) REVERT: P 455 LYS cc_start: 0.4642 (mttm) cc_final: 0.4286 (mptt) outliers start: 124 outliers final: 91 residues processed: 483 average time/residue: 0.4727 time to fit residues: 380.8696 Evaluate side-chains 465 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 366 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 280 HIS Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 197 MET Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 212 GLN Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 351 ILE Chi-restraints excluded: chain H residue 381 ASP Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 236 ASP Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 422 HIS Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 400 THR Chi-restraints excluded: chain P residue 443 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 271 optimal weight: 2.9990 chunk 436 optimal weight: 0.5980 chunk 266 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 303 optimal weight: 0.4980 chunk 458 optimal weight: 8.9990 chunk 421 optimal weight: 7.9990 chunk 364 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 281 optimal weight: 0.2980 chunk 223 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 HIS ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 HIS ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.4241 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: