Starting phenix.real_space_refine on Sun Sep 29 19:07:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xhn_33196/09_2024/7xhn_33196.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xhn_33196/09_2024/7xhn_33196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xhn_33196/09_2024/7xhn_33196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xhn_33196/09_2024/7xhn_33196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xhn_33196/09_2024/7xhn_33196.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xhn_33196/09_2024/7xhn_33196.cif" } resolution = 3.71 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= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 187 atoms to isotropic. 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 50 5.49 5 S 116 5.16 5 C 14740 2.51 5 N 4033 2.21 5 O 4425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23364 Number of models: 1 Model: "" Number of chains: 20 Chain: "o" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 95 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "H" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1560 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 4111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4111 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 15, 'TRANS': 501} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "K" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1869 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2422 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 288} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1298 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 7, 'TRANS': 160} Chain: "N" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2493 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "O" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1588 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "P" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1808 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 790 Classifications: {'peptide': 97} Link IDs: {'TRANS': 96} Chain: "T" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 804 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "W" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "X" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 590 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1175 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 699 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 479 Unresolved non-hydrogen angles: 594 Unresolved non-hydrogen dihedrals: 398 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 250 Chain: "R" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 308 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'TRANS': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 90 Time building chain proxies: 12.81, per 1000 atoms: 0.55 Number of scatterers: 23364 At special positions: 0 Unit cell: (106.14, 169.58, 187.88, 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 116 16.00 P 50 15.00 O 4425 8.00 N 4033 7.00 C 14740 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 - 3.00 Amino acid : True - 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: 5.88 Conformation dependent library (CDL) restraints added in 2.8 seconds 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5608 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 16 sheets defined 63.3% alpha, 5.7% beta 5 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 7.66 Creating SS restraints... Processing helix chain 'o' and resid 16 through 27 removed outlier: 3.746A pdb=" N ARG o 23 " --> pdb=" O ALA o 19 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU o 25 " --> pdb=" O LEU o 21 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR o 26 " --> pdb=" O GLU o 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 66 removed outlier: 3.626A pdb=" N LEU H 55 " --> pdb=" O LYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 Processing helix chain 'H' and resid 82 through 90 removed outlier: 5.094A pdb=" N GLU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE H 89 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 117 removed outlier: 3.942A pdb=" N ILE H 98 " --> pdb=" O VAL H 94 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 removed outlier: 3.868A pdb=" N ASP H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS H 132 " --> pdb=" O ASP H 128 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 188 removed outlier: 3.888A pdb=" N GLU H 152 " --> pdb=" O TRP H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 210 removed outlier: 4.337A pdb=" N ILE H 208 " --> pdb=" O MET H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 223 removed outlier: 3.795A pdb=" N GLY H 222 " --> pdb=" O ASN H 218 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER H 223 " --> pdb=" O LEU H 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 218 through 223' Processing helix chain 'H' and resid 232 through 237 Processing helix chain 'I' and resid 63 through 76 Processing helix chain 'I' and resid 84 through 100 removed outlier: 3.644A pdb=" N LEU I 88 " --> pdb=" O LYS I 84 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP I 100 " --> pdb=" O GLU I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 112 Processing helix chain 'I' and resid 122 through 129 Processing helix chain 'I' and resid 138 through 146 removed outlier: 3.539A pdb=" N ASP I 142 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL I 144 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL I 145 " --> pdb=" O GLU I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 171 Processing helix chain 'I' and resid 177 through 183 removed outlier: 3.938A pdb=" N ILE I 181 " --> pdb=" O ARG I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 removed outlier: 3.765A pdb=" N PHE I 188 " --> pdb=" O LEU I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 193 No H-bonds generated for 'chain 'I' and resid 191 through 193' Processing helix chain 'I' and resid 197 through 209 removed outlier: 4.174A pdb=" N HIS I 203 " --> pdb=" O PRO I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 214 Processing helix chain 'I' and resid 215 through 229 Processing helix chain 'I' and resid 232 through 245 Processing helix chain 'I' and resid 268 through 282 removed outlier: 4.572A pdb=" N ALA I 272 " --> pdb=" O LEU I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 379 removed outlier: 3.817A pdb=" N HIS I 374 " --> pdb=" O SER I 370 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR I 375 " --> pdb=" O LEU I 371 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE I 376 " --> pdb=" O LEU I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 402 removed outlier: 3.916A pdb=" N TRP I 391 " --> pdb=" O ARG I 387 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N CYS I 400 " --> pdb=" O LEU I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 405 No H-bonds generated for 'chain 'I' and resid 403 through 405' Processing helix chain 'I' and resid 409 through 429 removed outlier: 4.267A pdb=" N GLU I 413 " --> pdb=" O GLU I 409 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR I 415 " --> pdb=" O GLY I 411 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR I 420 " --> pdb=" O ASN I 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 443 removed outlier: 3.623A pdb=" N ALA I 437 " --> pdb=" O TYR I 433 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS I 441 " --> pdb=" O ALA I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 459 removed outlier: 3.848A pdb=" N GLN I 457 " --> pdb=" O SER I 453 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 514 removed outlier: 3.982A pdb=" N SER I 492 " --> pdb=" O TYR I 488 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRP I 507 " --> pdb=" O ASN I 503 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP I 511 " --> pdb=" O TRP I 507 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 551 removed outlier: 3.608A pdb=" N VAL I 533 " --> pdb=" O SER I 529 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR I 545 " --> pdb=" O GLY I 541 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR I 546 " --> pdb=" O TRP I 542 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET I 548 " --> pdb=" O SER I 544 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU I 551 " --> pdb=" O ALA I 547 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 566 Processing helix chain 'I' and resid 571 through 576 Processing helix chain 'I' and resid 584 through 593 removed outlier: 4.400A pdb=" N SER I 590 " --> pdb=" O GLY I 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 596 through 621 removed outlier: 4.279A pdb=" N GLN I 602 " --> pdb=" O SER I 598 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN I 620 " --> pdb=" O ALA I 616 " (cutoff:3.500A) Processing helix chain 'I' and resid 632 through 651 removed outlier: 3.675A pdb=" N MET I 647 " --> pdb=" O TYR I 643 " (cutoff:3.500A) Processing helix chain 'I' and resid 686 through 695 Processing helix chain 'I' and resid 716 through 726 Processing helix chain 'I' and resid 728 through 737 Processing helix chain 'K' and resid 21 through 46 removed outlier: 3.960A pdb=" N GLU K 27 " --> pdb=" O GLU K 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 75 removed outlier: 4.174A pdb=" N SER K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET K 62 " --> pdb=" O SER K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 147 removed outlier: 3.559A pdb=" N GLU K 105 " --> pdb=" O ARG K 101 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET K 106 " --> pdb=" O GLN K 102 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR K 110 " --> pdb=" O MET K 106 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 183 Processing helix chain 'K' and resid 183 through 188 Processing helix chain 'K' and resid 208 through 223 removed outlier: 3.792A pdb=" N ARG K 222 " --> pdb=" O ILE K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 249 removed outlier: 3.531A pdb=" N VAL K 243 " --> pdb=" O TRP K 239 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU K 247 " --> pdb=" O VAL K 243 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN K 249 " --> pdb=" O LEU K 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 40 removed outlier: 3.621A pdb=" N PHE L 40 " --> pdb=" O LYS L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 69 removed outlier: 4.406A pdb=" N HIS L 69 " --> pdb=" O ALA L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 105 removed outlier: 3.525A pdb=" N PHE L 98 " --> pdb=" O LEU L 94 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA L 101 " --> pdb=" O ALA L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 172 removed outlier: 4.043A pdb=" N GLU L 172 " --> pdb=" O ASP L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 205 removed outlier: 4.470A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 226 removed outlier: 3.830A pdb=" N THR L 226 " --> pdb=" O ALA L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 269 removed outlier: 3.603A pdb=" N VAL L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 296 removed outlier: 3.996A pdb=" N ARG L 293 " --> pdb=" O SER L 289 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS L 294 " --> pdb=" O HIS L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 302 Processing helix chain 'L' and resid 327 through 344 Processing helix chain 'M' and resid 25 through 38 removed outlier: 4.209A pdb=" N GLU M 38 " --> pdb=" O SER M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 83 Processing helix chain 'M' and resid 84 through 88 removed outlier: 3.797A pdb=" N VAL M 88 " --> pdb=" O LEU M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 124 removed outlier: 3.589A pdb=" N VAL M 117 " --> pdb=" O HIS M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 140 Processing helix chain 'M' and resid 142 through 154 removed outlier: 3.748A pdb=" N ARG M 148 " --> pdb=" O GLN M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 167 removed outlier: 3.623A pdb=" N LEU M 166 " --> pdb=" O ALA M 162 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER M 167 " --> pdb=" O LEU M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 14 Processing helix chain 'N' and resid 20 through 28 removed outlier: 3.663A pdb=" N ILE N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA N 27 " --> pdb=" O THR N 23 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP N 28 " --> pdb=" O ILE N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 39 removed outlier: 4.025A pdb=" N GLN N 37 " --> pdb=" O GLU N 33 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR N 38 " --> pdb=" O ASN N 34 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL N 39 " --> pdb=" O GLN N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 58 removed outlier: 4.084A pdb=" N ILE N 53 " --> pdb=" O VAL N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 76 removed outlier: 3.796A pdb=" N LEU N 68 " --> pdb=" O SER N 64 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE N 76 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 116 removed outlier: 4.019A pdb=" N ILE N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA N 115 " --> pdb=" O ILE N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 183 Processing helix chain 'N' and resid 197 through 206 removed outlier: 3.836A pdb=" N ALA N 203 " --> pdb=" O ASP N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 252 removed outlier: 3.685A pdb=" N ARG N 247 " --> pdb=" O VAL N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 308 Processing helix chain 'N' and resid 320 through 325 removed outlier: 3.556A pdb=" N THR N 324 " --> pdb=" O SER N 320 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 100 Processing helix chain 'O' and resid 100 through 109 removed outlier: 4.150A pdb=" N ILE O 104 " --> pdb=" O ASN O 100 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS O 109 " --> pdb=" O LEU O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 168 Processing helix chain 'O' and resid 176 through 184 removed outlier: 3.509A pdb=" N GLU O 182 " --> pdb=" O PHE O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 192 Processing helix chain 'O' and resid 192 through 200 removed outlier: 3.518A pdb=" N SER O 199 " --> pdb=" O ASP O 195 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP O 200 " --> pdb=" O ARG O 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 215 Processing helix chain 'O' and resid 261 through 278 removed outlier: 3.520A pdb=" N THR O 277 " --> pdb=" O THR O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 291 Processing helix chain 'O' and resid 292 through 295 removed outlier: 3.847A pdb=" N ASP O 295 " --> pdb=" O GLU O 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 292 through 295' Processing helix chain 'P' and resid 63 through 73 Processing helix chain 'P' and resid 90 through 94 removed outlier: 4.140A pdb=" N MET P 93 " --> pdb=" O SER P 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 148 Processing helix chain 'P' and resid 152 through 157 Processing helix chain 'P' and resid 165 through 191 removed outlier: 3.923A pdb=" N HIS P 171 " --> pdb=" O PHE P 167 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU P 175 " --> pdb=" O HIS P 171 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR P 183 " --> pdb=" O TYR P 179 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU P 189 " --> pdb=" O LYS P 185 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR P 191 " --> pdb=" O LEU P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 269 removed outlier: 4.198A pdb=" N ARG P 263 " --> pdb=" O PRO P 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR P 264 " --> pdb=" O LEU P 260 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY P 267 " --> pdb=" O ARG P 263 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 283 removed outlier: 3.625A pdb=" N LEU P 275 " --> pdb=" O ILE P 271 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 35 Processing helix chain 'S' and resid 43 through 72 removed outlier: 3.756A pdb=" N MET S 67 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA S 72 " --> pdb=" O PHE S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 86 removed outlier: 3.588A pdb=" N VAL S 82 " --> pdb=" O ASN S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 106 removed outlier: 3.641A pdb=" N ASP S 98 " --> pdb=" O LYS S 94 " (cutoff:3.500A) Processing helix chain 'T' and resid 459 through 472 Processing helix chain 'T' and resid 476 through 505 removed outlier: 3.707A pdb=" N MET T 482 " --> pdb=" O LYS T 478 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASP T 496 " --> pdb=" O GLN T 492 " (cutoff:3.500A) Processing helix chain 'T' and resid 511 through 522 removed outlier: 3.546A pdb=" N LEU T 515 " --> pdb=" O LYS T 511 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU T 518 " --> pdb=" O ASP T 514 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 removed outlier: 3.649A pdb=" N LEU T 534 " --> pdb=" O SER T 530 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG T 537 " --> pdb=" O VAL T 533 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS T 538 " --> pdb=" O LEU T 534 " (cutoff:3.500A) Processing helix chain 'T' and resid 540 through 548 removed outlier: 4.377A pdb=" N LEU T 546 " --> pdb=" O GLU T 542 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU T 547 " --> pdb=" O TYR T 543 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 30 removed outlier: 3.750A pdb=" N LEU W 22 " --> pdb=" O PRO W 18 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS W 23 " --> pdb=" O ARG W 19 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS W 30 " --> pdb=" O PHE W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 66 Processing helix chain 'W' and resid 71 through 86 removed outlier: 4.019A pdb=" N ALA W 77 " --> pdb=" O GLU W 73 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS W 80 " --> pdb=" O LEU W 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL W 81 " --> pdb=" O ALA W 77 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS W 84 " --> pdb=" O LYS W 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 23 removed outlier: 3.591A pdb=" N ARG X 17 " --> pdb=" O GLU X 13 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS X 22 " --> pdb=" O LEU X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 61 removed outlier: 3.768A pdb=" N LEU X 37 " --> pdb=" O ASP X 33 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 81 removed outlier: 3.911A pdb=" N LEU X 70 " --> pdb=" O ASP X 66 " (cutoff:3.500A) Proline residue: X 75 - end of helix removed outlier: 4.154A pdb=" N LEU X 79 " --> pdb=" O PRO X 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 100 Processing helix chain 'Q' and resid 102 through 121 Processing helix chain 'Q' and resid 131 through 195 Processing helix chain 'Q' and resid 226 through 231 removed outlier: 3.907A pdb=" N ALA Q 230 " --> pdb=" O LYS Q 226 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU Q 231 " --> pdb=" O GLU Q 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 226 through 231' Processing helix chain 'Q' and resid 236 through 268 removed outlier: 3.538A pdb=" N GLN Q 250 " --> pdb=" O HIS Q 246 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET Q 254 " --> pdb=" O GLN Q 250 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE Q 257 " --> pdb=" O SER Q 253 " (cutoff:3.500A) Processing helix chain 'U' and resid 250 through 268 Proline residue: U 256 - end of helix Processing helix chain 'U' and resid 271 through 366 removed outlier: 4.055A pdb=" N ILE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Proline residue: U 332 - end of helix removed outlier: 3.838A pdb=" N LEU U 351 " --> pdb=" O ARG U 347 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG U 352 " --> pdb=" O LYS U 348 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR U 356 " --> pdb=" O ARG U 352 " (cutoff:3.500A) Processing helix chain 'U' and resid 385 through 403 removed outlier: 3.786A pdb=" N LEU U 398 " --> pdb=" O ALA U 394 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 107 removed outlier: 3.665A pdb=" N GLU R 98 " --> pdb=" O GLU R 94 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU R 102 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE R 103 " --> pdb=" O GLU R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 113 Processing helix chain 'R' and resid 132 through 150 removed outlier: 4.417A pdb=" N MET R 143 " --> pdb=" O THR R 139 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS R 145 " --> pdb=" O GLU R 141 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN R 147 " --> pdb=" O MET R 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 253 through 254 Processing sheet with id=AA2, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'L' and resid 118 through 123 removed outlier: 3.611A pdb=" N GLN L 140 " --> pdb=" O ILE L 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 251 through 253 removed outlier: 5.956A pdb=" N SER L 242 " --> pdb=" O LEU L 304 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU L 304 " --> pdb=" O SER L 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 17 through 21 removed outlier: 6.716A pdb=" N THR M 17 " --> pdb=" O ILE M 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 47 through 48 Processing sheet with id=AA7, first strand: chain 'N' and resid 160 through 164 removed outlier: 6.342A pdb=" N TRP N 83 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU N 193 " --> pdb=" O TRP N 83 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL N 85 " --> pdb=" O MET N 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 120 through 122 removed outlier: 3.545A pdb=" N ALA N 136 " --> pdb=" O THR N 120 " (cutoff:3.500A) removed outlier: 11.213A pdb=" N VAL N 131 " --> pdb=" O TYR N 151 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N TYR N 151 " --> pdb=" O VAL N 131 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N ILE N 133 " --> pdb=" O PRO N 149 " (cutoff:3.500A) removed outlier: 10.641A pdb=" N ILE N 135 " --> pdb=" O TYR N 147 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N TYR N 147 " --> pdb=" O ILE N 135 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP N 137 " --> pdb=" O ASN N 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 267 through 269 removed outlier: 3.727A pdb=" N PHE N 297 " --> pdb=" O ALA N 267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 272 through 273 removed outlier: 3.992A pdb=" N THR N 273 " --> pdb=" O LEU N 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 114 through 116 removed outlier: 3.712A pdb=" N SER O 114 " --> pdb=" O CYS O 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 217 through 221 removed outlier: 3.747A pdb=" N THR O 253 " --> pdb=" O CYS O 234 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 78 through 86 removed outlier: 5.451A pdb=" N ILE P 78 " --> pdb=" O ASN P 110 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN P 110 " --> pdb=" O ILE P 78 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU P 123 " --> pdb=" O VAL P 135 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL P 135 " --> pdb=" O LEU P 123 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE P 125 " --> pdb=" O SER P 133 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER P 133 " --> pdb=" O ILE P 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 196 through 197 Processing sheet with id=AB6, first strand: chain 'P' and resid 221 through 222 Processing sheet with id=AB7, first strand: chain 'T' and resid 509 through 510 removed outlier: 3.550A pdb=" N VAL T 510 " --> pdb=" O ARG W 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 1308 hydrogen bonds defined for protein. 3837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 7.60 Time building geometry restraints manager: 6.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.32: 3851 1.32 - 1.60: 19744 1.60 - 1.88: 267 1.88 - 2.16: 0 2.16 - 2.44: 1 Bond restraints: 23863 Sorted by residual: bond pdb=" CB PRO O 208 " pdb=" CG PRO O 208 " ideal model delta sigma weight residual 1.492 2.440 -0.948 5.00e-02 4.00e+02 3.60e+02 bond pdb=" CA PRO K 259 " pdb=" CB PRO K 259 " ideal model delta sigma weight residual 1.531 1.623 -0.091 6.20e-03 2.60e+04 2.17e+02 bond pdb=" CG PRO O 208 " pdb=" CD PRO O 208 " ideal model delta sigma weight residual 1.503 1.035 0.468 3.40e-02 8.65e+02 1.90e+02 bond pdb=" CG LEU M 52 " pdb=" CD2 LEU M 52 " ideal model delta sigma weight residual 1.521 1.079 0.442 3.30e-02 9.18e+02 1.80e+02 bond pdb=" N PRO O 208 " pdb=" CA PRO O 208 " ideal model delta sigma weight residual 1.465 1.363 0.101 1.15e-02 7.56e+03 7.78e+01 ... (remaining 23858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 32473 21.21 - 42.42: 4 42.42 - 63.63: 0 63.63 - 84.84: 0 84.84 - 106.05: 1 Bond angle restraints: 32478 Sorted by residual: angle pdb=" CB PRO O 208 " pdb=" CG PRO O 208 " pdb=" CD PRO O 208 " ideal model delta sigma weight residual 106.10 0.05 106.05 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO O 208 " pdb=" N PRO O 208 " pdb=" CD PRO O 208 " ideal model delta sigma weight residual 112.00 82.02 29.98 1.40e+00 5.10e-01 4.59e+02 angle pdb=" CA PRO M 53 " pdb=" N PRO M 53 " pdb=" CD PRO M 53 " ideal model delta sigma weight residual 112.00 94.02 17.98 1.40e+00 5.10e-01 1.65e+02 angle pdb=" CA PRO O 208 " pdb=" CB PRO O 208 " pdb=" CG PRO O 208 " ideal model delta sigma weight residual 104.50 80.52 23.98 1.90e+00 2.77e-01 1.59e+02 angle pdb=" N PRO O 208 " pdb=" CD PRO O 208 " pdb=" CG PRO O 208 " ideal model delta sigma weight residual 103.20 84.53 18.67 1.50e+00 4.44e-01 1.55e+02 ... (remaining 32473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.71: 12561 22.71 - 45.42: 1471 45.42 - 68.14: 291 68.14 - 90.85: 41 90.85 - 113.56: 1 Dihedral angle restraints: 14365 sinusoidal: 5835 harmonic: 8530 Sorted by residual: dihedral pdb=" CD ARG P 168 " pdb=" NE ARG P 168 " pdb=" CZ ARG P 168 " pdb=" NH1 ARG P 168 " ideal model delta sinusoidal sigma weight residual 0.00 68.03 -68.03 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CD ARG H 47 " pdb=" NE ARG H 47 " pdb=" CZ ARG H 47 " pdb=" NH1 ARG H 47 " ideal model delta sinusoidal sigma weight residual 0.00 -63.46 63.46 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CA TYR T 552 " pdb=" C TYR T 552 " pdb=" N SER T 553 " pdb=" CA SER T 553 " ideal model delta harmonic sigma weight residual -180.00 -150.19 -29.81 0 5.00e+00 4.00e-02 3.56e+01 ... (remaining 14362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.174: 3752 0.174 - 0.347: 42 0.347 - 0.521: 1 0.521 - 0.694: 3 0.694 - 0.868: 1 Chirality restraints: 3799 Sorted by residual: chirality pdb=" CG LEU M 52 " pdb=" CB LEU M 52 " pdb=" CD1 LEU M 52 " pdb=" CD2 LEU M 52 " both_signs ideal model delta sigma weight residual False -2.59 -1.72 -0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" CG LEU I 558 " pdb=" CB LEU I 558 " pdb=" CD1 LEU I 558 " pdb=" CD2 LEU I 558 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CG LEU K 67 " pdb=" CB LEU K 67 " pdb=" CD1 LEU K 67 " pdb=" CD2 LEU K 67 " both_signs ideal model delta sigma weight residual False -2.59 -1.95 -0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 3796 not shown) Planarity restraints: 3940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 168 " -1.022 9.50e-02 1.11e+02 4.58e-01 1.27e+02 pdb=" NE ARG P 168 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG P 168 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG P 168 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG P 168 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 47 " 0.982 9.50e-02 1.11e+02 4.40e-01 1.17e+02 pdb=" NE ARG H 47 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG H 47 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG H 47 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 47 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 724 " 0.028 2.00e-02 2.50e+03 5.26e-02 4.85e+01 pdb=" CG PHE I 724 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE I 724 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE I 724 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE I 724 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 PHE I 724 " -0.078 2.00e-02 2.50e+03 pdb=" CZ PHE I 724 " 0.088 2.00e-02 2.50e+03 ... (remaining 3937 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 176 2.44 - 3.06: 16042 3.06 - 3.67: 39766 3.67 - 4.29: 56432 4.29 - 4.90: 87990 Nonbonded interactions: 200406 Sorted by model distance: nonbonded pdb=" OE1 GLN O 210 " pdb=" OG SER O 219 " model vdw 1.828 3.040 nonbonded pdb=" O ASN Q 181 " pdb=" NE2 GLN Q 184 " model vdw 1.912 3.120 nonbonded pdb=" CE MET P 165 " pdb=" CD ARG P 168 " model vdw 1.925 3.860 nonbonded pdb=" NH1 ARG Q 145 " pdb=" CB LYS U 308 " model vdw 1.928 3.520 nonbonded pdb=" OD2 ASP O 141 " pdb=" ND1 HIS O 151 " model vdw 2.017 3.120 ... (remaining 200401 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 53.830 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.100 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.948 23863 Z= 0.774 Angle : 1.258 106.053 32478 Z= 0.652 Chirality : 0.058 0.868 3799 Planarity : 0.012 0.458 3940 Dihedral : 19.322 113.560 8757 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 35.23 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.60 % Favored : 90.72 % Rotamer: Outliers : 1.25 % Allowed : 29.41 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.15), residues: 2814 helix: -1.24 (0.12), residues: 1632 sheet: -3.77 (0.31), residues: 195 loop : -2.54 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.004 TRP P 176 HIS 0.031 0.002 HIS Q 109 PHE 0.088 0.003 PHE I 724 TYR 0.105 0.003 TYR T 470 ARG 0.020 0.001 ARG X 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 434 time to evaluate : 2.656 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: 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: H 112 LEU cc_start: 0.8281 (tt) cc_final: 0.8068 (tp) outliers start: 29 outliers final: 18 residues processed: 445 average time/residue: 0.3667 time to fit residues: 247.2032 Evaluate side-chains 435 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 417 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain K residue 239 TRP Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 201 PHE Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 142 MET Chi-restraints excluded: chain T residue 470 TYR Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain T residue 536 GLU Chi-restraints excluded: chain X residue 38 MET Chi-restraints excluded: chain Q residue 83 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 223 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 0.0670 chunk 166 optimal weight: 0.5980 chunk 258 optimal weight: 2.9990 overall best weight: 0.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 ASN I 182 ASN I 213 ASN I 397 GLN I 495 GLN I 554 ASN I 641 ASN I 642 HIS I 726 GLN I 729 GLN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 GLN ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 290 HIS M 80 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 GLN N 106 ASN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 185 HIS N 208 GLN N 239 HIS ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 185 ASN O 210 GLN ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 532 HIS T 538 HIS X 56 GLN Q 109 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23863 Z= 0.251 Angle : 0.794 12.757 32478 Z= 0.406 Chirality : 0.045 0.279 3799 Planarity : 0.006 0.072 3940 Dihedral : 14.923 89.335 3609 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.85 % Favored : 91.72 % Rotamer: Outliers : 4.48 % Allowed : 24.33 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.61 (0.15), residues: 2814 helix: -0.89 (0.12), residues: 1733 sheet: -3.68 (0.32), residues: 184 loop : -2.77 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP H 148 HIS 0.015 0.001 HIS Q 109 PHE 0.032 0.002 PHE I 734 TYR 0.029 0.002 TYR I 440 ARG 0.009 0.001 ARG O 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 501 time to evaluate : 2.541 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: 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: H 154 LEU cc_start: 0.8165 (mt) cc_final: 0.7958 (mt) REVERT: H 189 MET cc_start: 0.6809 (mpp) cc_final: 0.6207 (mmt) REVERT: H 226 ASN cc_start: 0.7737 (t0) cc_final: 0.7528 (t0) REVERT: I 132 CYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7092 (p) REVERT: I 229 MET cc_start: 0.6386 (OUTLIER) cc_final: 0.6180 (mmm) REVERT: I 570 ASP cc_start: 0.6226 (p0) cc_final: 0.5958 (p0) REVERT: I 607 MET cc_start: 0.5675 (ppp) cc_final: 0.5429 (ppp) REVERT: L 31 LEU cc_start: 0.5526 (OUTLIER) cc_final: 0.5263 (mm) REVERT: L 71 GLN cc_start: 0.8024 (tp-100) cc_final: 0.7789 (tp40) REVERT: L 205 ASP cc_start: 0.8071 (t0) cc_final: 0.7789 (t0) REVERT: L 319 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6966 (pptt) REVERT: M 29 GLN cc_start: 0.7528 (tp40) cc_final: 0.7279 (tp40) REVERT: N 169 ARG cc_start: 0.6382 (mtm180) cc_final: 0.6088 (mtm180) REVERT: N 191 MET cc_start: 0.8162 (tpp) cc_final: 0.7850 (ttm) REVERT: O 296 MET cc_start: 0.6892 (mmt) cc_final: 0.6610 (mmm) REVERT: P 113 MET cc_start: 0.4713 (mpp) cc_final: 0.2966 (mmt) REVERT: P 136 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6921 (p) REVERT: P 165 MET cc_start: 0.6800 (mmp) cc_final: 0.5620 (mpp) REVERT: S 19 LEU cc_start: 0.8951 (mt) cc_final: 0.8261 (mt) REVERT: S 40 MET cc_start: 0.5856 (mmm) cc_final: 0.5591 (tpp) REVERT: S 52 GLU cc_start: 0.9113 (pt0) cc_final: 0.8714 (pp20) REVERT: S 53 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8211 (mm) REVERT: T 469 PHE cc_start: 0.4413 (m-10) cc_final: 0.3998 (t80) REVERT: T 495 CYS cc_start: 0.8450 (m) cc_final: 0.8190 (m) REVERT: W 82 ILE cc_start: 0.9058 (mt) cc_final: 0.8716 (mp) outliers start: 104 outliers final: 36 residues processed: 569 average time/residue: 0.3653 time to fit residues: 316.3939 Evaluate side-chains 466 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 424 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 502 GLN Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 253 THR Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain Q residue 137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 259 optimal weight: 8.9990 chunk 280 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 208 optimal weight: 0.0010 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 ASN I 495 GLN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 ASN K 132 GLN ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 ASN ** L 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 328 ASN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 23863 Z= 0.491 Angle : 0.890 14.822 32478 Z= 0.453 Chirality : 0.048 0.215 3799 Planarity : 0.006 0.070 3940 Dihedral : 14.790 88.411 3580 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.10 % Favored : 90.55 % Rotamer: Outliers : 6.80 % Allowed : 23.99 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % 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: -2.29 (0.15), residues: 2814 helix: -0.56 (0.12), residues: 1716 sheet: -3.85 (0.33), residues: 167 loop : -2.77 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP N 28 HIS 0.019 0.002 HIS Q 109 PHE 0.045 0.003 PHE K 97 TYR 0.032 0.003 TYR P 179 ARG 0.013 0.001 ARG I 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 425 time to evaluate : 2.379 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: 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: H 162 LEU cc_start: 0.8829 (tp) cc_final: 0.8620 (tp) REVERT: H 189 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6609 (mmt) REVERT: H 226 ASN cc_start: 0.8639 (t0) cc_final: 0.8322 (t0) REVERT: I 229 MET cc_start: 0.6811 (OUTLIER) cc_final: 0.6579 (mmm) REVERT: I 502 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: I 607 MET cc_start: 0.6028 (ppp) cc_final: 0.5359 (ppp) REVERT: I 642 HIS cc_start: 0.6606 (t-170) cc_final: 0.6236 (t-170) REVERT: I 651 LEU cc_start: 0.6964 (pp) cc_final: 0.6591 (pp) REVERT: I 691 TYR cc_start: 0.7236 (m-80) cc_final: 0.6818 (m-80) REVERT: I 726 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6584 (mm-40) REVERT: K 161 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8390 (pp20) REVERT: K 223 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.6897 (pp) REVERT: L 319 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6785 (pptt) REVERT: M 75 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8701 (ttpt) REVERT: M 79 GLN cc_start: 0.7612 (mp10) cc_final: 0.7401 (mp10) REVERT: N 191 MET cc_start: 0.8580 (tpp) cc_final: 0.8130 (ttm) REVERT: O 296 MET cc_start: 0.6878 (mmt) cc_final: 0.6439 (mmm) REVERT: P 179 TYR cc_start: 0.8187 (m-80) cc_final: 0.7912 (m-80) REVERT: S 13 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.8232 (t80) REVERT: S 33 GLU cc_start: 0.6881 (tt0) cc_final: 0.6194 (mt-10) REVERT: S 40 MET cc_start: 0.6173 (mmm) cc_final: 0.5790 (tpp) REVERT: T 469 PHE cc_start: 0.4010 (OUTLIER) cc_final: 0.3625 (t80) REVERT: T 473 MET cc_start: 0.8378 (ppp) cc_final: 0.8162 (ppp) REVERT: T 481 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8459 (mp0) REVERT: T 482 MET cc_start: 0.7511 (mmt) cc_final: 0.7118 (mmt) REVERT: T 485 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8152 (pttp) REVERT: W 49 LEU cc_start: 0.9172 (mt) cc_final: 0.8961 (mm) REVERT: X 43 LYS cc_start: 0.8409 (tttp) cc_final: 0.7540 (mttt) outliers start: 158 outliers final: 73 residues processed: 538 average time/residue: 0.3585 time to fit residues: 294.4556 Evaluate side-chains 472 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 387 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 502 GLN Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 689 LEU Chi-restraints excluded: chain I residue 726 GLN Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain I residue 731 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 322 ILE Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 263 GLN Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 141 ASP Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 175 HIS Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 137 ASP Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain P residue 256 GLU Chi-restraints excluded: chain P residue 283 CYS Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 469 PHE Chi-restraints excluded: chain T residue 470 TYR Chi-restraints excluded: chain T residue 481 GLU Chi-restraints excluded: chain T residue 485 LYS Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 189 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 0.0980 chunk 174 optimal weight: 0.5980 chunk 260 optimal weight: 1.9990 chunk 275 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 246 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 ASN I 559 HIS I 602 GLN ** L 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 23863 Z= 0.276 Angle : 0.789 13.694 32478 Z= 0.396 Chirality : 0.045 0.212 3799 Planarity : 0.005 0.064 3940 Dihedral : 14.473 89.713 3578 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.14 % Favored : 91.51 % Rotamer: Outliers : 5.43 % Allowed : 26.70 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.15), residues: 2814 helix: -0.40 (0.12), residues: 1730 sheet: -3.35 (0.36), residues: 161 loop : -2.77 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 148 HIS 0.007 0.001 HIS I 685 PHE 0.045 0.002 PHE Q 112 TYR 0.031 0.002 TYR P 179 ARG 0.007 0.001 ARG K 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 453 time to evaluate : 2.774 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 226 ASN cc_start: 0.8540 (t0) cc_final: 0.8209 (t0) REVERT: I 160 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8150 (p) REVERT: I 229 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.6041 (mmm) REVERT: I 428 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8453 (tt) REVERT: I 474 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8102 (tt) REVERT: I 502 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7615 (mm110) REVERT: I 566 GLU cc_start: 0.7580 (tt0) cc_final: 0.7297 (tt0) REVERT: I 642 HIS cc_start: 0.6579 (t-170) cc_final: 0.6329 (t-170) REVERT: K 161 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8406 (pp20) REVERT: K 223 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7109 (pp) REVERT: L 85 TYR cc_start: 0.7258 (m-80) cc_final: 0.7001 (m-80) REVERT: L 205 ASP cc_start: 0.8232 (t0) cc_final: 0.7802 (t0) REVERT: L 319 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6718 (pptt) REVERT: M 29 GLN cc_start: 0.7696 (tp40) cc_final: 0.7313 (tm-30) REVERT: M 75 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8450 (ttpt) REVERT: N 191 MET cc_start: 0.8379 (tpp) cc_final: 0.7930 (ttm) REVERT: O 196 ARG cc_start: 0.7859 (tpm170) cc_final: 0.7657 (tpm170) REVERT: O 296 MET cc_start: 0.6740 (mmt) cc_final: 0.6353 (mmm) REVERT: P 113 MET cc_start: 0.4814 (mpp) cc_final: 0.2640 (mmt) REVERT: S 40 MET cc_start: 0.5965 (mmm) cc_final: 0.5744 (tpp) REVERT: S 52 GLU cc_start: 0.9108 (pt0) cc_final: 0.8658 (pp20) REVERT: S 94 LYS cc_start: 0.9007 (pptt) cc_final: 0.8513 (tppt) REVERT: T 469 PHE cc_start: 0.4488 (OUTLIER) cc_final: 0.3853 (t80) REVERT: T 473 MET cc_start: 0.8305 (ppp) cc_final: 0.8098 (ppp) REVERT: T 481 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8553 (mp0) REVERT: T 485 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8636 (pttp) REVERT: X 43 LYS cc_start: 0.8419 (tttp) cc_final: 0.7923 (mttt) outliers start: 126 outliers final: 74 residues processed: 537 average time/residue: 0.3804 time to fit residues: 308.7672 Evaluate side-chains 489 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 403 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 502 GLN Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 695 PHE Chi-restraints excluded: chain I residue 731 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 322 ILE Chi-restraints excluded: chain L residue 325 HIS Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 258 ASP Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 175 HIS Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain P residue 256 GLU Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 469 PHE Chi-restraints excluded: chain T residue 470 TYR Chi-restraints excluded: chain T residue 477 ARG Chi-restraints excluded: chain T residue 481 GLU Chi-restraints excluded: chain T residue 485 LYS Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 20 HIS Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain Q residue 83 HIS Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 189 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 0.7980 chunk 156 optimal weight: 0.5980 chunk 4 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 190 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 185 ASN ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23863 Z= 0.282 Angle : 0.797 14.079 32478 Z= 0.399 Chirality : 0.045 0.227 3799 Planarity : 0.004 0.059 3940 Dihedral : 14.299 89.498 3576 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.46 % Favored : 91.22 % Rotamer: Outliers : 6.24 % Allowed : 26.79 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.16), residues: 2814 helix: -0.18 (0.12), residues: 1727 sheet: -3.29 (0.36), residues: 153 loop : -2.68 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 28 HIS 0.013 0.001 HIS K 255 PHE 0.037 0.002 PHE Q 112 TYR 0.018 0.002 TYR T 470 ARG 0.012 0.001 ARG H 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 439 time to evaluate : 2.610 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 226 ASN cc_start: 0.8515 (t0) cc_final: 0.8204 (t0) REVERT: I 229 MET cc_start: 0.6407 (OUTLIER) cc_final: 0.6006 (mmm) REVERT: I 428 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8437 (tt) REVERT: I 474 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.7994 (tt) REVERT: I 566 GLU cc_start: 0.7544 (tt0) cc_final: 0.7324 (tt0) REVERT: K 161 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8377 (pp20) REVERT: K 223 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.6972 (pp) REVERT: L 57 GLU cc_start: 0.5249 (OUTLIER) cc_final: 0.4860 (pt0) REVERT: L 85 TYR cc_start: 0.7381 (m-80) cc_final: 0.7154 (m-80) REVERT: L 205 ASP cc_start: 0.8217 (t0) cc_final: 0.8005 (t0) REVERT: L 319 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6729 (pptt) REVERT: M 29 GLN cc_start: 0.7721 (tp40) cc_final: 0.7346 (tm-30) REVERT: M 79 GLN cc_start: 0.7529 (mp10) cc_final: 0.7257 (mp10) REVERT: N 199 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7363 (t0) REVERT: O 187 TYR cc_start: 0.8479 (m-80) cc_final: 0.8140 (m-80) REVERT: O 196 ARG cc_start: 0.7860 (tpm170) cc_final: 0.7637 (tpm170) REVERT: O 296 MET cc_start: 0.6674 (mmt) cc_final: 0.6238 (mmm) REVERT: S 56 ARG cc_start: 0.8815 (mmm160) cc_final: 0.8598 (mmm160) REVERT: S 94 LYS cc_start: 0.8944 (pptt) cc_final: 0.8500 (tppt) REVERT: T 469 PHE cc_start: 0.4583 (OUTLIER) cc_final: 0.3852 (t80) REVERT: T 473 MET cc_start: 0.8296 (ppp) cc_final: 0.7963 (ppp) REVERT: T 485 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8686 (pttp) REVERT: T 488 ASP cc_start: 0.8136 (t0) cc_final: 0.7527 (m-30) REVERT: T 542 GLU cc_start: 0.8681 (pm20) cc_final: 0.8083 (pm20) REVERT: X 43 LYS cc_start: 0.8486 (tttp) cc_final: 0.7896 (mttt) REVERT: X 80 ASP cc_start: 0.8804 (t0) cc_final: 0.8561 (m-30) REVERT: X 81 PHE cc_start: 0.7987 (t80) cc_final: 0.7782 (t80) REVERT: Q 176 ILE cc_start: 0.6935 (mp) cc_final: 0.6636 (mm) outliers start: 145 outliers final: 89 residues processed: 536 average time/residue: 0.3548 time to fit residues: 290.4627 Evaluate side-chains 504 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 405 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 100 TRP Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 174 PHE Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 502 GLN Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 695 PHE Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain I residue 731 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 322 ILE Chi-restraints excluded: chain L residue 325 HIS Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 199 ASP Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 175 HIS Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 253 THR Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain P residue 256 GLU Chi-restraints excluded: chain P residue 283 CYS Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 469 PHE Chi-restraints excluded: chain T residue 470 TYR Chi-restraints excluded: chain T residue 477 ARG Chi-restraints excluded: chain T residue 485 LYS Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 20 HIS Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain c residue 266 PHE Chi-restraints excluded: chain Q residue 83 HIS Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 166 VAL Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 189 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 0.7980 chunk 248 optimal weight: 0.0370 chunk 54 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 228 optimal weight: 0.1980 chunk 127 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS I 642 HIS L 140 GLN ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23863 Z= 0.221 Angle : 0.793 14.127 32478 Z= 0.393 Chirality : 0.044 0.246 3799 Planarity : 0.004 0.061 3940 Dihedral : 14.176 89.125 3576 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.82 % Favored : 91.83 % Rotamer: Outliers : 5.60 % Allowed : 27.61 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.16), residues: 2814 helix: -0.01 (0.12), residues: 1730 sheet: -2.90 (0.38), residues: 159 loop : -2.61 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 148 HIS 0.011 0.001 HIS I 642 PHE 0.045 0.002 PHE K 97 TYR 0.021 0.002 TYR S 95 ARG 0.009 0.001 ARG Q 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 460 time to evaluate : 2.513 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 226 ASN cc_start: 0.8300 (t0) cc_final: 0.7944 (t0) REVERT: I 193 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: I 474 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7877 (tt) REVERT: I 506 LEU cc_start: 0.8449 (mm) cc_final: 0.8070 (mt) REVERT: I 566 GLU cc_start: 0.7285 (tt0) cc_final: 0.7057 (tt0) REVERT: K 161 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8316 (pt0) REVERT: L 85 TYR cc_start: 0.7265 (m-80) cc_final: 0.7022 (m-80) REVERT: L 319 LYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6620 (pptt) REVERT: O 187 TYR cc_start: 0.8441 (m-80) cc_final: 0.8151 (m-80) REVERT: O 296 MET cc_start: 0.6588 (mmt) cc_final: 0.6265 (mmm) REVERT: P 113 MET cc_start: 0.4651 (mpp) cc_final: 0.2567 (mmt) REVERT: S 94 LYS cc_start: 0.8946 (pptt) cc_final: 0.8420 (tppt) REVERT: T 469 PHE cc_start: 0.4817 (OUTLIER) cc_final: 0.4331 (m-10) REVERT: T 473 MET cc_start: 0.8262 (ppp) cc_final: 0.7867 (ppp) REVERT: T 488 ASP cc_start: 0.8053 (t0) cc_final: 0.7569 (m-30) REVERT: T 495 CYS cc_start: 0.8487 (m) cc_final: 0.8105 (m) REVERT: T 511 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8214 (mttp) REVERT: T 513 GLU cc_start: 0.8446 (pm20) cc_final: 0.8215 (pm20) REVERT: W 83 LEU cc_start: 0.8796 (pp) cc_final: 0.8403 (tt) REVERT: X 43 LYS cc_start: 0.8457 (tttp) cc_final: 0.7985 (mmtp) REVERT: X 80 ASP cc_start: 0.8798 (t0) cc_final: 0.8517 (m-30) REVERT: Q 162 ILE cc_start: 0.6430 (OUTLIER) cc_final: 0.6069 (tp) outliers start: 130 outliers final: 74 residues processed: 551 average time/residue: 0.3452 time to fit residues: 292.8976 Evaluate side-chains 484 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 403 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain I residue 100 TRP Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 174 PHE Chi-restraints excluded: chain I residue 193 GLN Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 493 VAL Chi-restraints excluded: chain I residue 502 GLN Chi-restraints excluded: chain I residue 559 HIS Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain I residue 731 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 217 GLU Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 325 HIS Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 28 TRP Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 253 THR Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain P residue 256 GLU Chi-restraints excluded: chain P residue 283 CYS Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 469 PHE Chi-restraints excluded: chain T residue 470 TYR Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain c residue 266 PHE Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain Q residue 166 VAL Chi-restraints excluded: chain Q residue 175 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 274 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN I 114 ASN ** I 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 641 ASN I 642 HIS I 726 GLN K 39 GLN ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 170 GLN ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 23863 Z= 0.365 Angle : 0.883 14.618 32478 Z= 0.435 Chirality : 0.048 0.480 3799 Planarity : 0.005 0.060 3940 Dihedral : 14.160 89.659 3576 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.32 % Favored : 91.29 % Rotamer: Outliers : 5.56 % Allowed : 28.21 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.16), residues: 2814 helix: 0.05 (0.12), residues: 1734 sheet: -2.97 (0.38), residues: 158 loop : -2.79 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 148 HIS 0.013 0.002 HIS P 171 PHE 0.030 0.002 PHE Q 112 TYR 0.019 0.002 TYR T 490 ARG 0.008 0.001 ARG I 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 405 time to evaluate : 2.833 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 141 MET cc_start: 0.4111 (ptt) cc_final: 0.3871 (ptt) REVERT: H 226 ASN cc_start: 0.8503 (t0) cc_final: 0.8143 (t0) REVERT: I 133 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6927 (pmm) REVERT: I 193 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7827 (mt0) REVERT: I 403 TYR cc_start: 0.5887 (OUTLIER) cc_final: 0.4413 (m-10) REVERT: I 474 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8061 (tt) REVERT: I 566 GLU cc_start: 0.7488 (tt0) cc_final: 0.7181 (tt0) REVERT: K 161 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8376 (pp20) REVERT: K 217 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: K 223 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7197 (pp) REVERT: L 85 TYR cc_start: 0.7354 (m-80) cc_final: 0.7147 (m-80) REVERT: L 319 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6649 (pptt) REVERT: N 199 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7514 (t0) REVERT: N 263 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7979 (tm-30) REVERT: O 187 TYR cc_start: 0.8557 (m-80) cc_final: 0.8200 (m-80) REVERT: O 282 GLN cc_start: 0.7354 (pm20) cc_final: 0.7152 (pm20) REVERT: P 93 MET cc_start: 0.0554 (ptt) cc_final: -0.0383 (ptt) REVERT: P 113 MET cc_start: 0.4415 (mpp) cc_final: 0.2354 (mmt) REVERT: S 33 GLU cc_start: 0.6866 (tt0) cc_final: 0.6162 (mt-10) REVERT: S 56 ARG cc_start: 0.8896 (mmm160) cc_final: 0.8660 (mmm160) REVERT: S 94 LYS cc_start: 0.9022 (pptt) cc_final: 0.8443 (tppt) REVERT: T 469 PHE cc_start: 0.4844 (OUTLIER) cc_final: 0.4308 (m-10) REVERT: T 473 MET cc_start: 0.8260 (ppp) cc_final: 0.7805 (ppp) REVERT: T 488 ASP cc_start: 0.8074 (t0) cc_final: 0.7572 (m-30) REVERT: T 511 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8060 (mttp) REVERT: T 513 GLU cc_start: 0.8604 (pm20) cc_final: 0.8396 (pm20) REVERT: W 83 LEU cc_start: 0.8882 (pp) cc_final: 0.8577 (mp) REVERT: X 43 LYS cc_start: 0.8492 (tttp) cc_final: 0.7874 (mmpt) REVERT: X 74 LEU cc_start: 0.9087 (mt) cc_final: 0.8583 (pp) outliers start: 129 outliers final: 87 residues processed: 498 average time/residue: 0.3543 time to fit residues: 274.9703 Evaluate side-chains 482 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 384 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain I residue 100 TRP Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 193 GLN Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 403 TYR Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 502 GLN Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 726 GLN Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain I residue 731 LEU Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 217 GLU Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 28 TRP Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 199 ASP Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 141 ASP Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 170 GLN Chi-restraints excluded: chain O residue 175 HIS Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 253 THR Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain P residue 256 GLU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain T residue 469 PHE Chi-restraints excluded: chain T residue 470 TYR Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 64 ARG Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain Q residue 83 HIS Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 189 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 164 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 25 optimal weight: 0.0170 chunk 215 optimal weight: 7.9990 chunk 249 optimal weight: 7.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 27 GLN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 642 HIS I 726 GLN ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 139 ASN S 57 GLN ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23863 Z= 0.240 Angle : 0.861 16.305 32478 Z= 0.419 Chirality : 0.046 0.432 3799 Planarity : 0.004 0.062 3940 Dihedral : 14.090 89.824 3576 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.78 % Favored : 91.86 % Rotamer: Outliers : 4.61 % Allowed : 28.98 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2814 helix: 0.10 (0.12), residues: 1730 sheet: -2.86 (0.38), residues: 161 loop : -2.74 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP H 148 HIS 0.020 0.001 HIS Q 109 PHE 0.033 0.002 PHE Q 112 TYR 0.017 0.002 TYR L 81 ARG 0.008 0.001 ARG Q 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 425 time to evaluate : 2.525 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: 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: H 127 MET cc_start: 0.5444 (ttp) cc_final: 0.4957 (tmm) REVERT: H 148 TRP cc_start: 0.5929 (m-90) cc_final: 0.5516 (m-90) REVERT: H 162 LEU cc_start: 0.8690 (tp) cc_final: 0.8381 (tp) REVERT: H 204 MET cc_start: 0.7499 (tmm) cc_final: 0.7175 (tmm) REVERT: H 226 ASN cc_start: 0.8388 (t0) cc_final: 0.8092 (t0) REVERT: I 193 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7725 (mt0) REVERT: I 474 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8025 (tt) REVERT: I 506 LEU cc_start: 0.8507 (mm) cc_final: 0.8256 (mt) REVERT: I 566 GLU cc_start: 0.7169 (tt0) cc_final: 0.6681 (tt0) REVERT: K 161 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8288 (pp20) REVERT: K 239 TRP cc_start: 0.8133 (t-100) cc_final: 0.7872 (t-100) REVERT: L 220 TRP cc_start: 0.7990 (m100) cc_final: 0.6811 (t60) REVERT: L 224 MET cc_start: 0.7075 (mtm) cc_final: 0.6513 (mtp) REVERT: L 319 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6650 (pptt) REVERT: M 170 ARG cc_start: 0.6981 (ttm110) cc_final: 0.6708 (tmm160) REVERT: O 187 TYR cc_start: 0.8504 (m-80) cc_final: 0.8192 (m-80) REVERT: P 93 MET cc_start: 0.0357 (ptt) cc_final: 0.0027 (pmm) REVERT: P 113 MET cc_start: 0.4393 (mpp) cc_final: 0.2486 (mmt) REVERT: S 52 GLU cc_start: 0.9104 (pt0) cc_final: 0.8750 (pp20) REVERT: S 94 LYS cc_start: 0.8996 (pptt) cc_final: 0.8403 (tppt) REVERT: T 469 PHE cc_start: 0.4905 (OUTLIER) cc_final: 0.4403 (m-10) REVERT: T 478 LYS cc_start: 0.9306 (ptpt) cc_final: 0.8625 (tttm) REVERT: T 495 CYS cc_start: 0.8537 (m) cc_final: 0.8170 (m) REVERT: T 511 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7959 (mttp) REVERT: W 83 LEU cc_start: 0.8803 (pp) cc_final: 0.8395 (tt) REVERT: X 43 LYS cc_start: 0.8450 (tttp) cc_final: 0.7939 (mmpt) outliers start: 107 outliers final: 75 residues processed: 502 average time/residue: 0.3418 time to fit residues: 264.7007 Evaluate side-chains 475 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 394 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 100 TRP Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 193 GLN Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 502 GLN Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 642 HIS Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 726 GLN Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 325 HIS Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 28 TRP Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain P residue 229 ASP Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain P residue 256 GLU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain T residue 469 PHE Chi-restraints excluded: chain T residue 470 TYR Chi-restraints excluded: chain T residue 477 ARG Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain Q residue 83 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 30.0000 chunk 240 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 154 optimal weight: 0.0870 chunk 111 optimal weight: 0.4980 chunk 201 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 270 optimal weight: 5.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 726 GLN ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 170 GLN ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23863 Z= 0.275 Angle : 0.891 16.320 32478 Z= 0.434 Chirality : 0.047 0.415 3799 Planarity : 0.005 0.060 3940 Dihedral : 14.090 89.387 3576 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.21 % Favored : 91.47 % Rotamer: Outliers : 4.65 % Allowed : 29.46 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 2814 helix: 0.12 (0.12), residues: 1734 sheet: -2.71 (0.38), residues: 161 loop : -2.77 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP L 225 HIS 0.013 0.002 HIS Q 109 PHE 0.051 0.002 PHE P 172 TYR 0.019 0.002 TYR I 722 ARG 0.008 0.001 ARG S 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 417 time to evaluate : 2.436 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: 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: H 127 MET cc_start: 0.5269 (ttp) cc_final: 0.4731 (tmm) REVERT: H 226 ASN cc_start: 0.8384 (t0) cc_final: 0.8135 (t0) REVERT: I 193 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7650 (mt0) REVERT: I 403 TYR cc_start: 0.5920 (OUTLIER) cc_final: 0.4286 (m-10) REVERT: I 474 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.7925 (tt) REVERT: I 506 LEU cc_start: 0.8578 (mm) cc_final: 0.8325 (mt) REVERT: I 566 GLU cc_start: 0.7341 (tt0) cc_final: 0.6926 (tt0) REVERT: K 35 MET cc_start: 0.5609 (ptt) cc_final: 0.5388 (ptt) REVERT: K 161 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8339 (pp20) REVERT: L 85 TYR cc_start: 0.7334 (m-80) cc_final: 0.7126 (m-80) REVERT: L 319 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6490 (pptt) REVERT: M 170 ARG cc_start: 0.7074 (ttm110) cc_final: 0.6728 (tmm160) REVERT: N 199 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7363 (t0) REVERT: N 333 TYR cc_start: 0.6436 (t80) cc_final: 0.5178 (t80) REVERT: O 187 TYR cc_start: 0.8540 (m-80) cc_final: 0.8200 (m-80) REVERT: O 193 GLN cc_start: 0.6651 (tm-30) cc_final: 0.6338 (pp30) REVERT: O 296 MET cc_start: 0.7178 (mmm) cc_final: 0.6209 (mmm) REVERT: P 93 MET cc_start: 0.0323 (ptt) cc_final: -0.0104 (pmm) REVERT: P 113 MET cc_start: 0.4411 (mpp) cc_final: 0.2502 (mmt) REVERT: S 94 LYS cc_start: 0.9003 (pptt) cc_final: 0.8333 (tppt) REVERT: T 469 PHE cc_start: 0.4937 (OUTLIER) cc_final: 0.4401 (m-10) REVERT: T 473 MET cc_start: 0.8022 (ppp) cc_final: 0.7804 (ppp) REVERT: T 478 LYS cc_start: 0.9249 (ptpt) cc_final: 0.8622 (tttp) REVERT: T 488 ASP cc_start: 0.8109 (t0) cc_final: 0.7649 (m-30) REVERT: T 495 CYS cc_start: 0.8554 (m) cc_final: 0.8181 (m) REVERT: T 511 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8345 (mttp) REVERT: W 83 LEU cc_start: 0.8775 (pp) cc_final: 0.8379 (tt) REVERT: X 43 LYS cc_start: 0.8490 (tttp) cc_final: 0.7968 (mmtp) outliers start: 108 outliers final: 82 residues processed: 497 average time/residue: 0.3495 time to fit residues: 267.7861 Evaluate side-chains 490 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 400 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain I residue 100 TRP Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 193 GLN Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 403 TYR Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 502 GLN Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 217 GLU Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 325 HIS Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 28 TRP Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 199 ASP Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 170 GLN Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 253 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain P residue 256 GLU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain T residue 469 PHE Chi-restraints excluded: chain T residue 470 TYR Chi-restraints excluded: chain T residue 477 ARG Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 64 ARG Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 81 PHE Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain Q residue 83 HIS Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 166 VAL Chi-restraints excluded: chain Q residue 175 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 3.9990 chunk 128 optimal weight: 0.0030 chunk 188 optimal weight: 0.9980 chunk 283 optimal weight: 30.0000 chunk 261 optimal weight: 0.0000 chunk 226 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 174 optimal weight: 0.0070 chunk 138 optimal weight: 0.6980 chunk 179 optimal weight: 0.7980 chunk 240 optimal weight: 0.8980 overall best weight: 0.3012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 642 HIS K 160 ASN ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 170 GLN ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23863 Z= 0.223 Angle : 0.897 15.827 32478 Z= 0.435 Chirality : 0.047 0.414 3799 Planarity : 0.005 0.064 3940 Dihedral : 14.064 89.872 3576 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.68 % Favored : 92.00 % Rotamer: Outliers : 3.66 % Allowed : 31.01 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.16), residues: 2814 helix: 0.20 (0.12), residues: 1722 sheet: -2.71 (0.37), residues: 172 loop : -2.64 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP L 225 HIS 0.011 0.001 HIS K 255 PHE 0.044 0.002 PHE P 172 TYR 0.030 0.002 TYR O 192 ARG 0.009 0.001 ARG I 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 439 time to evaluate : 2.605 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: 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: H 127 MET cc_start: 0.4968 (ttp) cc_final: 0.4464 (tmm) REVERT: H 148 TRP cc_start: 0.5701 (m-90) cc_final: 0.5183 (m-90) REVERT: H 226 ASN cc_start: 0.8062 (t0) cc_final: 0.7808 (t0) REVERT: I 193 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7607 (mt0) REVERT: I 403 TYR cc_start: 0.5818 (OUTLIER) cc_final: 0.3724 (m-10) REVERT: I 506 LEU cc_start: 0.8294 (mm) cc_final: 0.8017 (mt) REVERT: I 566 GLU cc_start: 0.7112 (tt0) cc_final: 0.6682 (tt0) REVERT: L 319 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6532 (pptt) REVERT: O 187 TYR cc_start: 0.8504 (m-80) cc_final: 0.8231 (m-80) REVERT: O 296 MET cc_start: 0.7058 (mmm) cc_final: 0.6397 (tpt) REVERT: P 93 MET cc_start: 0.0304 (ptt) cc_final: -0.0100 (pmm) REVERT: P 113 MET cc_start: 0.4582 (mpp) cc_final: 0.2699 (mmt) REVERT: S 94 LYS cc_start: 0.9037 (pptt) cc_final: 0.8336 (tppt) REVERT: T 469 PHE cc_start: 0.4887 (OUTLIER) cc_final: 0.4330 (m-10) REVERT: T 473 MET cc_start: 0.7949 (ppp) cc_final: 0.7645 (ppp) REVERT: T 478 LYS cc_start: 0.9179 (ptpt) cc_final: 0.8601 (tttm) REVERT: T 488 ASP cc_start: 0.8029 (t0) cc_final: 0.7668 (m-30) REVERT: T 495 CYS cc_start: 0.8413 (m) cc_final: 0.8100 (m) REVERT: T 542 GLU cc_start: 0.8367 (pm20) cc_final: 0.8061 (pm20) REVERT: T 550 CYS cc_start: 0.5276 (m) cc_final: 0.5048 (p) REVERT: W 68 ARG cc_start: 0.7391 (ttp-110) cc_final: 0.6947 (ttp-110) REVERT: W 83 LEU cc_start: 0.8722 (pp) cc_final: 0.8327 (tt) REVERT: X 43 LYS cc_start: 0.8210 (tttp) cc_final: 0.7859 (mmpt) REVERT: X 74 LEU cc_start: 0.9085 (mt) cc_final: 0.8516 (tp) outliers start: 85 outliers final: 71 residues processed: 499 average time/residue: 0.3480 time to fit residues: 266.2312 Evaluate side-chains 479 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 404 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 100 TRP Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 193 GLN Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 403 TYR Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 502 GLN Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 642 HIS Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 217 GLU Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 220 TRP Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 325 HIS Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain P residue 229 ASP Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain P residue 256 GLU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain T residue 469 PHE Chi-restraints excluded: chain T residue 470 TYR Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 64 ARG Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 81 PHE Chi-restraints excluded: chain Q residue 83 HIS Chi-restraints excluded: chain Q residue 166 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.6259 > 50: distance: 9 - 17: 3.008 distance: 75 - 80: 26.644 distance: 80 - 81: 40.375 distance: 81 - 82: 10.458 distance: 81 - 84: 38.447 distance: 82 - 83: 36.296 distance: 82 - 88: 4.687 distance: 84 - 85: 28.323 distance: 85 - 86: 13.304 distance: 85 - 87: 36.043 distance: 88 - 89: 41.871 distance: 89 - 90: 7.124 distance: 89 - 92: 36.437 distance: 90 - 91: 23.482 distance: 90 - 95: 24.105 distance: 92 - 93: 24.362 distance: 92 - 94: 18.230 distance: 95 - 96: 50.225 distance: 96 - 97: 57.945 distance: 96 - 99: 24.775 distance: 97 - 98: 31.927 distance: 97 - 102: 44.419 distance: 99 - 100: 12.526 distance: 99 - 101: 33.760 distance: 102 - 103: 34.770 distance: 103 - 104: 52.671 distance: 103 - 106: 41.437 distance: 104 - 105: 43.577 distance: 104 - 110: 37.336 distance: 106 - 107: 31.320 distance: 107 - 108: 43.905 distance: 107 - 109: 34.096 distance: 110 - 111: 38.698 distance: 111 - 112: 37.866 distance: 111 - 114: 41.532 distance: 112 - 113: 8.528 distance: 112 - 121: 12.545 distance: 114 - 115: 51.276 distance: 115 - 116: 29.008 distance: 115 - 117: 26.330 distance: 116 - 118: 20.044 distance: 117 - 119: 35.195 distance: 118 - 120: 20.427 distance: 119 - 120: 19.197 distance: 121 - 122: 18.982 distance: 121 - 127: 33.374 distance: 122 - 123: 43.781 distance: 122 - 125: 39.191 distance: 123 - 124: 60.358 distance: 123 - 128: 48.368 distance: 124 - 147: 37.850 distance: 125 - 126: 26.120 distance: 126 - 127: 40.061 distance: 128 - 129: 21.922 distance: 128 - 134: 30.714 distance: 129 - 130: 28.577 distance: 129 - 132: 22.916 distance: 130 - 131: 33.274 distance: 130 - 135: 38.083 distance: 131 - 158: 31.844 distance: 132 - 133: 28.358 distance: 133 - 134: 8.502 distance: 135 - 136: 35.506 distance: 136 - 137: 22.407 distance: 137 - 138: 5.345 distance: 137 - 139: 20.962 distance: 139 - 140: 45.458 distance: 140 - 141: 41.795 distance: 140 - 143: 31.561 distance: 141 - 142: 21.353 distance: 141 - 147: 20.376 distance: 142 - 176: 7.296 distance: 143 - 144: 22.161 distance: 143 - 145: 27.878 distance: 144 - 146: 36.808 distance: 147 - 148: 42.253 distance: 148 - 149: 37.614 distance: 148 - 151: 31.809 distance: 149 - 150: 29.366 distance: 149 - 158: 23.543 distance: 150 - 181: 13.642 distance: 151 - 152: 18.035 distance: 152 - 153: 18.292 distance: 152 - 154: 20.089 distance: 153 - 155: 5.174 distance: 154 - 156: 7.330 distance: 155 - 157: 7.904 distance: 156 - 157: 9.927