Starting phenix.real_space_refine on Sat Dec 16 12:29:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgr_25116/12_2023/7sgr_25116_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgr_25116/12_2023/7sgr_25116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgr_25116/12_2023/7sgr_25116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgr_25116/12_2023/7sgr_25116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgr_25116/12_2023/7sgr_25116_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgr_25116/12_2023/7sgr_25116_updated.pdb" } resolution = 2.9 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= -0.001 sd= 0.104 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 6 5.49 5 S 80 5.16 5 C 22817 2.51 5 N 5907 2.21 5 O 6179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 34989 Number of models: 1 Model: "" Number of chains: 21 Chain: "J" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4505 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 552} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 5549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5549 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 679} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 5543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5543 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 679} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4509 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 17, 'TRANS': 552} Chain: "E" Number of atoms: 5535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5535 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 679} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4509 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 17, 'TRANS': 552} Chain: "H" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "L" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "D" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "C" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1035 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "G" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1026 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 131 Chain: "K" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "J" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 82 Unusual residues: {'6OU': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'6OU:plan-1': 4, '6OU:plan-2': 6, '6OU:plan-3': 6} Unresolved non-hydrogen planarities: 60 Chain: "I" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 131 Unusual residues: {'6OU': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'6OU:plan-1': 7, '6OU:plan-2': 8, '6OU:plan-3': 8} Unresolved non-hydrogen planarities: 90 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Unusual residues: {'6OU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'6OU:plan-1': 6, '6OU:plan-2': 3, '6OU:plan-3': 3} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'6OU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 2, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Unusual residues: {'6OU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'6OU:plan-1': 4, '6OU:plan-2': 4, '6OU:plan-3': 4} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'6OU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 2, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'6OU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'6OU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 2, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 18.09, per 1000 atoms: 0.52 Number of scatterers: 34989 At special positions: 0 Unit cell: (146.59, 149.8, 173.34, 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 80 16.00 P 6 15.00 O 6179 8.00 N 5907 7.00 C 22817 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: 13.65 Conformation dependent library (CDL) restraints added in 6.2 seconds 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 175 helices and 22 sheets defined 58.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.13 Creating SS restraints... Processing helix chain 'J' and resid 142 through 149 removed outlier: 4.015A pdb=" N ALA J 146 " --> pdb=" O TRP J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 181 removed outlier: 4.074A pdb=" N GLU J 156 " --> pdb=" O LYS J 152 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR J 171 " --> pdb=" O PHE J 167 " (cutoff:3.500A) Proline residue: J 172 - end of helix Processing helix chain 'J' and resid 189 through 236 removed outlier: 3.616A pdb=" N VAL J 200 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG J 222 " --> pdb=" O HIS J 218 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 244 Processing helix chain 'J' and resid 248 through 265 removed outlier: 4.126A pdb=" N LEU J 258 " --> pdb=" O ARG J 254 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP J 259 " --> pdb=" O VAL J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 277 Processing helix chain 'J' and resid 280 through 289 Processing helix chain 'J' and resid 291 through 338 Proline residue: J 302 - end of helix Proline residue: J 313 - end of helix Processing helix chain 'J' and resid 340 through 345 Processing helix chain 'J' and resid 350 through 401 Processing helix chain 'J' and resid 407 through 428 Proline residue: J 423 - end of helix Processing helix chain 'J' and resid 431 through 448 Processing helix chain 'J' and resid 508 through 515 removed outlier: 3.597A pdb=" N LEU J 511 " --> pdb=" O LYS J 508 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR J 512 " --> pdb=" O SER J 509 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE J 515 " --> pdb=" O THR J 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 544 Processing helix chain 'J' and resid 559 through 563 Processing helix chain 'J' and resid 572 through 581 Processing helix chain 'J' and resid 584 through 589 Processing helix chain 'J' and resid 594 through 596 No H-bonds generated for 'chain 'J' and resid 594 through 596' Processing helix chain 'J' and resid 608 through 621 Processing helix chain 'J' and resid 638 through 646 Processing helix chain 'J' and resid 648 through 651 No H-bonds generated for 'chain 'J' and resid 648 through 651' Processing helix chain 'J' and resid 687 through 691 Processing helix chain 'J' and resid 697 through 705 Processing helix chain 'I' and resid 9 through 20 Processing helix chain 'I' and resid 27 through 34 Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 66 through 69 Processing helix chain 'I' and resid 111 through 117 Processing helix chain 'I' and resid 140 through 149 Proline residue: I 145 - end of helix Processing helix chain 'I' and resid 151 through 181 Proline residue: I 172 - end of helix removed outlier: 3.907A pdb=" N PHE I 175 " --> pdb=" O THR I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 236 removed outlier: 3.597A pdb=" N VAL I 193 " --> pdb=" O SER I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 244 Processing helix chain 'I' and resid 248 through 265 removed outlier: 4.104A pdb=" N LEU I 258 " --> pdb=" O ARG I 254 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP I 259 " --> pdb=" O VAL I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 277 Processing helix chain 'I' and resid 280 through 289 removed outlier: 3.606A pdb=" N ALA I 284 " --> pdb=" O PHE I 280 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL I 285 " --> pdb=" O ILE I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 291 through 338 removed outlier: 4.172A pdb=" N VAL I 296 " --> pdb=" O LYS I 292 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE I 297 " --> pdb=" O LEU I 293 " (cutoff:3.500A) Proline residue: I 302 - end of helix Proline residue: I 313 - end of helix Processing helix chain 'I' and resid 340 through 345 Processing helix chain 'I' and resid 349 through 402 Processing helix chain 'I' and resid 407 through 448 Proline residue: I 423 - end of helix removed outlier: 3.667A pdb=" N ILE I 430 " --> pdb=" O ARG I 426 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLN I 432 " --> pdb=" O ALA I 428 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP I 433 " --> pdb=" O GLN I 429 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR I 442 " --> pdb=" O GLY I 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 515 No H-bonds generated for 'chain 'I' and resid 512 through 515' Processing helix chain 'I' and resid 538 through 544 removed outlier: 3.899A pdb=" N GLN I 544 " --> pdb=" O TRP I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 563 Processing helix chain 'I' and resid 572 through 581 Processing helix chain 'I' and resid 585 through 590 Processing helix chain 'I' and resid 594 through 596 No H-bonds generated for 'chain 'I' and resid 594 through 596' Processing helix chain 'I' and resid 608 through 621 Processing helix chain 'I' and resid 641 through 651 removed outlier: 4.412A pdb=" N LYS I 650 " --> pdb=" O ARG I 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 687 through 691 Processing helix chain 'I' and resid 697 through 705 Processing helix chain 'A' and resid 9 through 21 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'A' and resid 140 through 181 removed outlier: 3.848A pdb=" N ILE A 144 " --> pdb=" O THR A 141 " (cutoff:3.500A) Proline residue: A 145 - end of helix removed outlier: 4.195A pdb=" N ILE A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS A 149 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LYS A 152 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR A 171 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 190 through 237 Processing helix chain 'A' and resid 240 through 245 removed outlier: 3.962A pdb=" N SER A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 removed outlier: 4.336A pdb=" N LEU A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 289 removed outlier: 3.837A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 337 Proline residue: A 302 - end of helix Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 349 through 402 Processing helix chain 'A' and resid 407 through 448 removed outlier: 3.976A pdb=" N VAL A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA A 422 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 4.177A pdb=" N GLN A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 435 " --> pdb=" O TRP A 431 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 515 No H-bonds generated for 'chain 'A' and resid 512 through 515' Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 538 through 544 removed outlier: 3.758A pdb=" N ARG A 543 " --> pdb=" O ASN A 539 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN A 544 " --> pdb=" O TRP A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 585 through 590 Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 638 through 651 removed outlier: 4.608A pdb=" N HIS A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LYS A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 667 removed outlier: 3.695A pdb=" N VAL A 667 " --> pdb=" O LEU A 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 664 through 667' Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 697 through 705 Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 151 through 181 Proline residue: B 172 - end of helix Processing helix chain 'B' and resid 188 through 237 removed outlier: 3.540A pdb=" N VAL B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 248 through 265 removed outlier: 4.644A pdb=" N LEU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 289 removed outlier: 4.670A pdb=" N PHE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B 282 " --> pdb=" O PHE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 338 removed outlier: 3.739A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Proline residue: B 302 - end of helix Proline residue: B 313 - end of helix Processing helix chain 'B' and resid 340 through 345 Processing helix chain 'B' and resid 349 through 402 Processing helix chain 'B' and resid 407 through 448 Proline residue: B 423 - end of helix removed outlier: 4.197A pdb=" N ALA B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLN B 429 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 435 " --> pdb=" O TRP B 431 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 515 removed outlier: 3.672A pdb=" N LEU B 511 " --> pdb=" O LYS B 508 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR B 512 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 513 " --> pdb=" O THR B 510 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 515 " --> pdb=" O THR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 538 through 544 Processing helix chain 'B' and resid 559 through 563 Processing helix chain 'B' and resid 572 through 582 Processing helix chain 'B' and resid 585 through 590 removed outlier: 3.766A pdb=" N GLU B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 596 No H-bonds generated for 'chain 'B' and resid 594 through 596' Processing helix chain 'B' and resid 608 through 619 Processing helix chain 'B' and resid 641 through 651 removed outlier: 4.713A pdb=" N HIS B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS B 650 " --> pdb=" O ARG B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 691 Processing helix chain 'B' and resid 697 through 705 Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 43 through 53 Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 111 through 117 Processing helix chain 'E' and resid 140 through 149 Proline residue: E 145 - end of helix Processing helix chain 'E' and resid 151 through 181 removed outlier: 3.667A pdb=" N ILE E 170 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR E 171 " --> pdb=" O PHE E 167 " (cutoff:3.500A) Proline residue: E 172 - end of helix Processing helix chain 'E' and resid 191 through 237 removed outlier: 3.537A pdb=" N ALA E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 245 Processing helix chain 'E' and resid 248 through 265 removed outlier: 4.373A pdb=" N LEU E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 277 Processing helix chain 'E' and resid 280 through 289 removed outlier: 3.571A pdb=" N VAL E 285 " --> pdb=" O ILE E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 338 removed outlier: 3.718A pdb=" N VAL E 296 " --> pdb=" O LYS E 292 " (cutoff:3.500A) Proline residue: E 302 - end of helix Proline residue: E 313 - end of helix Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 349 through 401 Processing helix chain 'E' and resid 407 through 448 Proline residue: E 423 - end of helix removed outlier: 3.743A pdb=" N ILE E 430 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLN E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP E 433 " --> pdb=" O GLN E 429 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL E 447 " --> pdb=" O ARG E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 533 through 535 No H-bonds generated for 'chain 'E' and resid 533 through 535' Processing helix chain 'E' and resid 538 through 543 Processing helix chain 'E' and resid 559 through 563 Processing helix chain 'E' and resid 572 through 582 Processing helix chain 'E' and resid 585 through 589 Processing helix chain 'E' and resid 608 through 621 removed outlier: 3.806A pdb=" N GLN E 612 " --> pdb=" O GLY E 608 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG E 613 " --> pdb=" O GLY E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 634 No H-bonds generated for 'chain 'E' and resid 632 through 634' Processing helix chain 'E' and resid 638 through 651 removed outlier: 4.575A pdb=" N HIS E 649 " --> pdb=" O MET E 645 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LYS E 650 " --> pdb=" O ARG E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 667 Processing helix chain 'E' and resid 687 through 691 Processing helix chain 'E' and resid 697 through 705 Processing helix chain 'F' and resid 141 through 149 Proline residue: F 145 - end of helix Processing helix chain 'F' and resid 151 through 181 Proline residue: F 172 - end of helix Processing helix chain 'F' and resid 190 through 237 removed outlier: 3.596A pdb=" N ILE F 223 " --> pdb=" O SER F 219 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA F 237 " --> pdb=" O ARG F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 244 Processing helix chain 'F' and resid 248 through 265 removed outlier: 3.964A pdb=" N ARG F 254 " --> pdb=" O ASP F 250 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL F 255 " --> pdb=" O THR F 251 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 277 Processing helix chain 'F' and resid 280 through 289 removed outlier: 3.784A pdb=" N TYR F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 338 Proline residue: F 302 - end of helix Proline residue: F 313 - end of helix Processing helix chain 'F' and resid 340 through 345 Processing helix chain 'F' and resid 350 through 401 Processing helix chain 'F' and resid 407 through 428 Proline residue: F 423 - end of helix Processing helix chain 'F' and resid 431 through 448 Processing helix chain 'F' and resid 512 through 515 No H-bonds generated for 'chain 'F' and resid 512 through 515' Processing helix chain 'F' and resid 533 through 535 No H-bonds generated for 'chain 'F' and resid 533 through 535' Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 559 through 563 Processing helix chain 'F' and resid 572 through 582 Processing helix chain 'F' and resid 585 through 590 Processing helix chain 'F' and resid 594 through 596 No H-bonds generated for 'chain 'F' and resid 594 through 596' Processing helix chain 'F' and resid 601 through 603 No H-bonds generated for 'chain 'F' and resid 601 through 603' Processing helix chain 'F' and resid 608 through 621 Processing helix chain 'F' and resid 638 through 651 removed outlier: 4.535A pdb=" N ILE F 643 " --> pdb=" O GLU F 639 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N HIS F 649 " --> pdb=" O MET F 645 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LYS F 650 " --> pdb=" O ARG F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 691 Processing helix chain 'F' and resid 697 through 705 Processing helix chain 'H' and resid 11 through 24 Processing helix chain 'H' and resid 36 through 40 Processing helix chain 'H' and resid 44 through 50 removed outlier: 3.662A pdb=" N LEU H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 76 Processing helix chain 'L' and resid 11 through 24 Processing helix chain 'L' and resid 36 through 40 Processing helix chain 'L' and resid 44 through 49 removed outlier: 3.817A pdb=" N LEU L 48 " --> pdb=" O ALA L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 76 Processing helix chain 'D' and resid 10 through 23 Processing helix chain 'D' and resid 36 through 40 Processing helix chain 'D' and resid 44 through 50 removed outlier: 3.693A pdb=" N LEU D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 76 Processing helix chain 'C' and resid 35 through 41 Processing helix chain 'C' and resid 43 through 48 removed outlier: 3.506A pdb=" N LEU C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 77 Processing helix chain 'C' and resid 374 through 379 Processing helix chain 'C' and resid 395 through 398 No H-bonds generated for 'chain 'C' and resid 395 through 398' Processing helix chain 'C' and resid 459 through 469 Proline residue: C 466 - end of helix Processing helix chain 'G' and resid 35 through 41 removed outlier: 3.535A pdb=" N PHE G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 60 through 77 Processing helix chain 'G' and resid 374 through 379 Processing helix chain 'G' and resid 395 through 398 No H-bonds generated for 'chain 'G' and resid 395 through 398' Processing helix chain 'G' and resid 459 through 472 removed outlier: 3.941A pdb=" N SER G 465 " --> pdb=" O TYR G 462 " (cutoff:3.500A) Proline residue: G 466 - end of helix Processing helix chain 'K' and resid 35 through 41 removed outlier: 3.716A pdb=" N GLU K 40 " --> pdb=" O LYS K 36 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE K 41 " --> pdb=" O ASP K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 48 Processing helix chain 'K' and resid 59 through 75 Processing sheet with id= A, first strand: chain 'J' and resid 490 through 492 Processing sheet with id= B, first strand: chain 'J' and resid 680 through 685 removed outlier: 7.111A pdb=" N VAL J 675 " --> pdb=" O VAL J 682 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLN J 684 " --> pdb=" O ILE J 673 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE J 673 " --> pdb=" O GLN J 684 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG J 672 " --> pdb=" O VAL J 497 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL J 657 " --> pdb=" O ILE J 498 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE J 500 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE J 659 " --> pdb=" O ILE J 500 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'I' and resid 55 through 61 Processing sheet with id= D, first strand: chain 'I' and resid 74 through 76 removed outlier: 3.540A pdb=" N PHE I 84 " --> pdb=" O VAL I 76 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'I' and resid 96 through 100 removed outlier: 3.545A pdb=" N ASN I 105 " --> pdb=" O ASP I 100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 490 through 492 Processing sheet with id= G, first strand: chain 'I' and resid 680 through 685 removed outlier: 6.995A pdb=" N VAL I 675 " --> pdb=" O VAL I 682 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN I 684 " --> pdb=" O ILE I 673 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE I 673 " --> pdb=" O GLN I 684 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG I 672 " --> pdb=" O VAL I 497 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL I 657 " --> pdb=" O ILE I 498 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE I 500 " --> pdb=" O VAL I 657 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE I 659 " --> pdb=" O ILE I 500 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N GLY I 502 " --> pdb=" O ILE I 659 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 56 through 61 Processing sheet with id= I, first strand: chain 'A' and resid 74 through 76 removed outlier: 3.764A pdb=" N PHE A 84 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 97 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL A 89 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG A 95 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 96 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 468 through 470 Processing sheet with id= K, first strand: chain 'A' and resid 680 through 683 removed outlier: 7.024A pdb=" N VAL A 675 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 672 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL A 657 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE A 500 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 659 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N GLY A 502 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 468 through 471 removed outlier: 3.620A pdb=" N ARG B 471 " --> pdb=" O GLN B 525 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 680 through 685 removed outlier: 7.314A pdb=" N VAL B 675 " --> pdb=" O VAL B 682 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN B 684 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 673 " --> pdb=" O GLN B 684 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 672 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 657 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE B 500 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 659 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 56 through 61 removed outlier: 3.524A pdb=" N ILE E 122 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 74 through 76 removed outlier: 3.634A pdb=" N PHE E 84 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL E 89 " --> pdb=" O ARG E 95 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ARG E 95 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 490 through 492 Processing sheet with id= Q, first strand: chain 'E' and resid 680 through 685 removed outlier: 7.100A pdb=" N VAL E 675 " --> pdb=" O VAL E 682 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN E 684 " --> pdb=" O ILE E 673 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 673 " --> pdb=" O GLN E 684 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 490 through 492 Processing sheet with id= S, first strand: chain 'F' and resid 681 through 685 removed outlier: 7.174A pdb=" N VAL F 675 " --> pdb=" O VAL F 682 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN F 684 " --> pdb=" O ILE F 673 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE F 673 " --> pdb=" O GLN F 684 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY F 502 " --> pdb=" O ALA F 661 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 79 through 81 Processing sheet with id= U, first strand: chain 'C' and resid 403 through 405 Processing sheet with id= V, first strand: chain 'G' and resid 403 through 405 1872 hydrogen bonds defined for protein. 5385 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: 13.59 Time building geometry restraints manager: 14.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5530 1.29 - 1.42: 8850 1.42 - 1.55: 20850 1.55 - 1.68: 224 1.68 - 1.81: 148 Bond restraints: 35602 Sorted by residual: bond pdb=" C40 6OU J 802 " pdb=" C41 6OU J 802 " ideal model delta sigma weight residual 1.333 1.559 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C40 6OU L 401 " pdb=" C41 6OU L 401 " ideal model delta sigma weight residual 1.333 1.559 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C40 6OU I 801 " pdb=" C41 6OU I 801 " ideal model delta sigma weight residual 1.333 1.558 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C40 6OU J 801 " pdb=" C41 6OU J 801 " ideal model delta sigma weight residual 1.333 1.558 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C40 6OU A 802 " pdb=" C41 6OU A 802 " ideal model delta sigma weight residual 1.333 1.558 -0.225 2.00e-02 2.50e+03 1.26e+02 ... (remaining 35597 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.59: 514 105.59 - 112.72: 19731 112.72 - 119.85: 11438 119.85 - 126.99: 16076 126.99 - 134.12: 347 Bond angle restraints: 48106 Sorted by residual: angle pdb=" N GLY F 403 " pdb=" CA GLY F 403 " pdb=" C GLY F 403 " ideal model delta sigma weight residual 115.30 125.45 -10.15 1.39e+00 5.18e-01 5.33e+01 angle pdb=" C40 6OU L 401 " pdb=" C41 6OU L 401 " pdb=" C42 6OU L 401 " ideal model delta sigma weight residual 127.56 108.43 19.13 3.00e+00 1.11e-01 4.07e+01 angle pdb=" C40 6OU J 802 " pdb=" C41 6OU J 802 " pdb=" C42 6OU J 802 " ideal model delta sigma weight residual 127.56 109.24 18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" C40 6OU F 802 " pdb=" C41 6OU F 802 " pdb=" C42 6OU F 802 " ideal model delta sigma weight residual 127.56 109.26 18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" C40 6OU J 801 " pdb=" C41 6OU J 801 " pdb=" C42 6OU J 801 " ideal model delta sigma weight residual 127.56 109.95 17.61 3.00e+00 1.11e-01 3.45e+01 ... (remaining 48101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 20931 33.71 - 67.42: 458 67.42 - 101.13: 67 101.13 - 134.84: 3 134.84 - 168.55: 8 Dihedral angle restraints: 21467 sinusoidal: 8691 harmonic: 12776 Sorted by residual: dihedral pdb=" CA VAL F 348 " pdb=" C VAL F 348 " pdb=" N SER F 349 " pdb=" CA SER F 349 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" C19 6OU A 801 " pdb=" C20 6OU A 801 " pdb=" C21 6OU A 801 " pdb=" O22 6OU A 801 " ideal model delta sinusoidal sigma weight residual 301.00 132.45 168.55 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C19 6OU K 401 " pdb=" C20 6OU K 401 " pdb=" C21 6OU K 401 " pdb=" O22 6OU K 401 " ideal model delta sinusoidal sigma weight residual -59.00 108.54 -167.54 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 21464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 5427 0.098 - 0.196: 212 0.196 - 0.294: 7 0.294 - 0.392: 1 0.392 - 0.491: 2 Chirality restraints: 5649 Sorted by residual: chirality pdb=" CA LEU A 301 " pdb=" N LEU A 301 " pdb=" C LEU A 301 " pdb=" CB LEU A 301 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CA PHE A 299 " pdb=" N PHE A 299 " pdb=" C PHE A 299 " pdb=" CB PHE A 299 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA ASP F 404 " pdb=" N ASP F 404 " pdb=" C ASP F 404 " pdb=" CB ASP F 404 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 5646 not shown) Planarity restraints: 6007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C39 6OU L 401 " -0.262 2.00e-02 2.50e+03 2.94e-01 8.64e+02 pdb=" C40 6OU L 401 " 0.477 2.00e-02 2.50e+03 pdb=" C41 6OU L 401 " -0.222 2.00e-02 2.50e+03 pdb=" C42 6OU L 401 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C39 6OU F 802 " 0.241 2.00e-02 2.50e+03 2.91e-01 8.45e+02 pdb=" C40 6OU F 802 " -0.459 2.00e-02 2.50e+03 pdb=" C41 6OU F 802 " 0.259 2.00e-02 2.50e+03 pdb=" C42 6OU F 802 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C39 6OU A 802 " 0.227 2.00e-02 2.50e+03 2.88e-01 8.29e+02 pdb=" C40 6OU A 802 " -0.444 2.00e-02 2.50e+03 pdb=" C41 6OU A 802 " 0.281 2.00e-02 2.50e+03 pdb=" C42 6OU A 802 " -0.063 2.00e-02 2.50e+03 ... (remaining 6004 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2945 2.74 - 3.28: 35236 3.28 - 3.82: 57149 3.82 - 4.36: 66477 4.36 - 4.90: 117469 Nonbonded interactions: 279276 Sorted by model distance: nonbonded pdb=" OE1 GLU I 257 " pdb=" OG SER I 440 " model vdw 2.202 2.440 nonbonded pdb=" O LEU E 41 " pdb=" OG SER E 45 " model vdw 2.220 2.440 nonbonded pdb=" OE1 GLU E 257 " pdb=" OG SER E 440 " model vdw 2.222 2.440 nonbonded pdb=" OE1 GLN J 176 " pdb=" OH TYR J 289 " model vdw 2.232 2.440 nonbonded pdb=" OG SER E 692 " pdb=" OE2 GLU E 693 " model vdw 2.238 2.440 ... (remaining 279271 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' and (resid 7 through 130 or (resid 131 through 132 and (name N or nam \ e CA or name C or name O or name CB )) or resid 133 through 454 or (resid 455 th \ rough 456 and (name N or name CA or name C or name O or name CB )) or resid 457 \ or (resid 458 and (name N or name CA or name C or name O or name CB )) or resid \ 459 through 706)) selection = (chain 'E' and (resid 7 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 136 or (resid 137 and (name N or na \ me CA or name C or name O or name CB )) or resid 138 through 706)) selection = (chain 'I' and (resid 7 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 130 or (resid 131 through 132 and ( \ name N or name CA or name C or name O or name CB )) or (resid 133 through 137 an \ d (name N or name CA or name C or name O or name CB )) or resid 138 through 454 \ or (resid 455 through 456 and (name N or name CA or name C or name O or name CB \ )) or resid 457 through 706)) } ncs_group { reference = (chain 'B' and (resid 137 through 687 or (resid 688 and (name N or name CA or na \ me C or name O or name CB )) or resid 689 through 706 or resid 801)) selection = (chain 'F' and (resid 137 through 687 or (resid 688 and (name N or name CA or na \ me C or name O or name CB )) or resid 689 through 706 or (resid 801 and (name C3 \ 1 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name C45))) \ ) selection = (chain 'J' and (resid 137 through 706 or (resid 801 and (name C31 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43 or name C44 or name C45)))) } ncs_group { reference = (chain 'C' and (resid 29 through 80 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 363 through 471)) selection = (chain 'G' and resid 29 through 471) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 9 through 77) selection = (chain 'L' and resid 9 through 77) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 14.010 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 91.490 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 0.226 35602 Z= 0.471 Angle : 0.792 19.128 48106 Z= 0.385 Chirality : 0.043 0.491 5649 Planarity : 0.009 0.294 6007 Dihedral : 15.212 168.546 13195 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.13), residues: 4369 helix: 1.80 (0.10), residues: 2658 sheet: -0.94 (0.29), residues: 346 loop : -1.43 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.001 TRP B 431 HIS 0.004 0.001 HIS E 662 PHE 0.030 0.001 PHE A 278 TYR 0.013 0.001 TYR C 462 ARG 0.007 0.000 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 702 time to evaluate : 4.053 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 702 average time/residue: 1.4131 time to fit residues: 1198.1365 Evaluate side-chains 436 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 435 time to evaluate : 4.136 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 5.6670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 367 optimal weight: 2.9990 chunk 329 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 112 optimal weight: 0.1980 chunk 222 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 340 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 395 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 103 GLN I 185 HIS I 385 GLN I 398 HIS I 552 ASN I 612 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN A 467 ASN A 523 ASN B 192 ASN B 472 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 121 HIS E 192 ASN E 268 GLN E 398 HIS E 525 GLN ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 622 ASN ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35602 Z= 0.282 Angle : 0.576 12.423 48106 Z= 0.298 Chirality : 0.043 0.235 5649 Planarity : 0.004 0.067 6007 Dihedral : 11.363 164.575 5260 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.65 % Allowed : 11.38 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.13), residues: 4369 helix: 1.57 (0.10), residues: 2677 sheet: -0.91 (0.28), residues: 367 loop : -1.27 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 431 HIS 0.005 0.001 HIS B 218 PHE 0.025 0.002 PHE J 587 TYR 0.019 0.001 TYR E 700 ARG 0.008 0.001 ARG F 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 456 time to evaluate : 4.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 37 residues processed: 508 average time/residue: 1.3115 time to fit residues: 815.6933 Evaluate side-chains 439 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 402 time to evaluate : 4.220 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 20 residues processed: 17 average time/residue: 0.5579 time to fit residues: 20.3244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 219 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 328 optimal weight: 0.0980 chunk 268 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 395 optimal weight: 8.9990 chunk 427 optimal weight: 40.0000 chunk 352 optimal weight: 0.8980 chunk 392 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 185 HIS I 385 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN A 260 GLN A 330 GLN A 449 ASN A 467 ASN B 523 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 GLN ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 622 ASN F 185 HIS F 585 HIS F 642 HIS C 39 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35602 Z= 0.234 Angle : 0.516 11.465 48106 Z= 0.269 Chirality : 0.042 0.219 5649 Planarity : 0.004 0.049 6007 Dihedral : 10.334 167.174 5260 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.08 % Allowed : 13.60 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.13), residues: 4369 helix: 1.66 (0.10), residues: 2675 sheet: -0.77 (0.27), residues: 364 loop : -1.24 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 431 HIS 0.005 0.001 HIS F 642 PHE 0.017 0.001 PHE L 41 TYR 0.020 0.001 TYR E 700 ARG 0.011 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 432 time to evaluate : 4.519 Fit side-chains outliers start: 113 outliers final: 57 residues processed: 491 average time/residue: 1.2980 time to fit residues: 784.5863 Evaluate side-chains 453 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 396 time to evaluate : 4.038 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 30 residues processed: 27 average time/residue: 0.3492 time to fit residues: 22.4679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 390 optimal weight: 0.8980 chunk 297 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 397 optimal weight: 5.9990 chunk 420 optimal weight: 20.0000 chunk 207 optimal weight: 0.6980 chunk 376 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 192 ASN I 185 HIS I 385 GLN A 185 HIS A 330 GLN A 467 ASN B 523 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN E 268 GLN ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 622 ASN ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35602 Z= 0.209 Angle : 0.501 13.934 48106 Z= 0.261 Chirality : 0.041 0.210 5649 Planarity : 0.004 0.043 6007 Dihedral : 9.699 165.384 5260 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.11 % Allowed : 15.29 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.13), residues: 4369 helix: 1.73 (0.10), residues: 2680 sheet: -0.56 (0.27), residues: 360 loop : -1.18 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 431 HIS 0.004 0.001 HIS F 218 PHE 0.017 0.001 PHE L 41 TYR 0.019 0.001 TYR J 700 ARG 0.010 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 420 time to evaluate : 4.151 Fit side-chains outliers start: 114 outliers final: 61 residues processed: 485 average time/residue: 1.3461 time to fit residues: 802.9424 Evaluate side-chains 456 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 395 time to evaluate : 4.013 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 38 residues processed: 25 average time/residue: 0.4956 time to fit residues: 25.0868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 350 optimal weight: 0.0570 chunk 238 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 313 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 358 optimal weight: 0.0870 chunk 290 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 377 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 185 HIS I 185 HIS I 329 ASN I 385 GLN I 602 GLN A 260 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN B 523 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 GLN E 268 GLN E 429 GLN ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 622 ASN ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35602 Z= 0.157 Angle : 0.479 12.368 48106 Z= 0.249 Chirality : 0.040 0.209 5649 Planarity : 0.003 0.050 6007 Dihedral : 9.028 165.203 5260 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.95 % Allowed : 16.11 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.13), residues: 4369 helix: 1.89 (0.10), residues: 2675 sheet: -0.41 (0.28), residues: 356 loop : -1.08 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 431 HIS 0.003 0.001 HIS F 218 PHE 0.013 0.001 PHE I 175 TYR 0.020 0.001 TYR J 700 ARG 0.011 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 425 time to evaluate : 4.083 Fit side-chains outliers start: 108 outliers final: 66 residues processed: 498 average time/residue: 1.3089 time to fit residues: 805.7386 Evaluate side-chains 452 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 386 time to evaluate : 4.127 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 46 residues processed: 22 average time/residue: 0.5928 time to fit residues: 25.1233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 141 optimal weight: 0.6980 chunk 378 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 420 optimal weight: 30.0000 chunk 349 optimal weight: 0.6980 chunk 194 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 139 optimal weight: 0.1980 chunk 220 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 487 ASN J 552 ASN J 612 GLN I 185 HIS I 385 GLN I 419 GLN I 602 GLN A 260 GLN A 330 GLN A 467 ASN A 647 ASN B 523 ASN B 552 ASN B 612 GLN B 705 GLN ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 567 ASN E 622 ASN ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 703 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35602 Z= 0.183 Angle : 0.487 10.286 48106 Z= 0.254 Chirality : 0.041 0.187 5649 Planarity : 0.003 0.054 6007 Dihedral : 8.815 163.937 5260 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.62 % Allowed : 17.12 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.13), residues: 4369 helix: 1.93 (0.10), residues: 2679 sheet: -0.35 (0.27), residues: 362 loop : -1.07 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 431 HIS 0.004 0.001 HIS F 218 PHE 0.026 0.001 PHE A 278 TYR 0.020 0.001 TYR J 700 ARG 0.011 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 407 time to evaluate : 4.258 Fit side-chains revert: symmetry clash outliers start: 96 outliers final: 63 residues processed: 473 average time/residue: 1.3075 time to fit residues: 763.1264 Evaluate side-chains 458 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 395 time to evaluate : 4.477 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 46 residues processed: 18 average time/residue: 0.5371 time to fit residues: 20.8636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 405 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 307 optimal weight: 3.9990 chunk 238 optimal weight: 0.0670 chunk 354 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 chunk 419 optimal weight: 8.9990 chunk 262 optimal weight: 0.6980 chunk 255 optimal weight: 0.6980 chunk 193 optimal weight: 5.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 487 ASN I 111 GLN I 185 HIS I 385 GLN I 602 GLN A 260 GLN A 330 GLN A 467 ASN B 523 ASN B 552 ASN E 429 GLN ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 622 ASN ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 703 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35602 Z= 0.159 Angle : 0.477 10.609 48106 Z= 0.248 Chirality : 0.040 0.229 5649 Planarity : 0.003 0.054 6007 Dihedral : 8.570 162.628 5260 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.24 % Allowed : 17.85 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.13), residues: 4369 helix: 1.97 (0.10), residues: 2687 sheet: -0.31 (0.27), residues: 362 loop : -0.99 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 431 HIS 0.004 0.001 HIS I 185 PHE 0.015 0.001 PHE H 63 TYR 0.021 0.001 TYR J 700 ARG 0.013 0.000 ARG I 592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 414 time to evaluate : 4.212 Fit side-chains outliers start: 82 outliers final: 52 residues processed: 480 average time/residue: 1.2664 time to fit residues: 751.9655 Evaluate side-chains 438 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 386 time to evaluate : 3.120 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 43 residues processed: 10 average time/residue: 0.4047 time to fit residues: 10.7451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 259 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 250 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 266 optimal weight: 7.9990 chunk 285 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 329 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: