Starting phenix.real_space_refine on Wed Sep 25 08:38:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpe_18548/09_2024/8qpe_18548.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpe_18548/09_2024/8qpe_18548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpe_18548/09_2024/8qpe_18548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpe_18548/09_2024/8qpe_18548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpe_18548/09_2024/8qpe_18548.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpe_18548/09_2024/8qpe_18548.cif" } resolution = 3.1 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 242 5.49 5 S 224 5.16 5 C 33730 2.51 5 N 9632 2.21 5 O 10738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 54566 Number of models: 1 Model: "" Number of chains: 21 Chain: "4" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1342 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p_pur': 24, 'rna3p_pyr': 24} Link IDs: {'rna2p': 15, 'rna3p': 47} Chain: "5" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2420 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 8, 'rna3p_pur': 39, 'rna3p_pyr': 58} Link IDs: {'rna2p': 17, 'rna3p': 97} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 926 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 23, 'rna3p_pyr': 15} Link IDs: {'rna2p': 5, 'rna3p': 37} Chain: "7" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 650 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "C" Number of atoms: 6592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6592 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 48, 'TRANS': 787} Chain: "D" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1170 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "I" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1513 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 7, 'TRANS': 175} Chain: "K" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 159 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 93 Chain: "M" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 962 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 117} Chain: "U" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3742 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 432} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "X" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 657 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "r" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 728 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "z1" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 239 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "z2" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 90 Classifications: {'RNA': 4} Modifications used: {'rna3p_pur': 4} Link IDs: {'rna3p': 3} Chain: "J" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1806 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2871 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 14, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 45 Chain: "F" Number of atoms: 3194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3194 Classifications: {'peptide': 404} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 387} Chain breaks: 1 Chain: "N" Number of atoms: 6071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6071 Classifications: {'peptide': 831} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 36, 'TRANS': 794} Chain breaks: 3 Unresolved non-hydrogen bonds: 650 Unresolved non-hydrogen angles: 826 Unresolved non-hydrogen dihedrals: 562 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 7, 'HIS:plan': 7, 'PHE:plan': 5, 'GLU:plan': 22, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 424 Chain: "A" Number of atoms: 18231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2247, 18231 Classifications: {'peptide': 2247} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PCIS': 3, 'PTRANS': 124, 'TRANS': 2119} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 265 Chain: "S" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1167 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.85, per 1000 atoms: 0.46 Number of scatterers: 54566 At special positions: 0 Unit cell: (213.3, 233.55, 206.55, 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 224 16.00 P 242 15.00 O 10738 8.00 N 9632 7.00 C 33730 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: 11.55 Conformation dependent library (CDL) restraints added in 6.0 seconds 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11892 Finding SS restraints... Secondary structure from input PDB file: 255 helices and 55 sheets defined 50.7% alpha, 12.0% beta 56 base pairs and 131 stacking pairs defined. Time for finding SS restraints: 18.48 Creating SS restraints... Processing helix chain '7' and resid 424 through 433 Processing helix chain '7' and resid 435 through 450 removed outlier: 3.820A pdb=" N LEU 7 439 " --> pdb=" O ASP 7 435 " (cutoff:3.500A) Processing helix chain '7' and resid 458 through 473 Processing helix chain 'C' and resid 117 through 124 removed outlier: 4.005A pdb=" N ASP C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 127 No H-bonds generated for 'chain 'C' and resid 125 through 127' Processing helix chain 'C' and resid 141 through 154 Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.795A pdb=" N VAL C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 261 through 266 Processing helix chain 'C' and resid 270 through 293 Processing helix chain 'C' and resid 295 through 299 removed outlier: 3.691A pdb=" N LEU C 298 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 299 " --> pdb=" O GLU C 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 295 through 299' Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 335 through 341 removed outlier: 3.717A pdb=" N LYS C 341 " --> pdb=" O GLN C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 373 through 386 removed outlier: 3.694A pdb=" N VAL C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 428 through 437 Processing helix chain 'C' and resid 440 through 453 removed outlier: 4.864A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix Processing helix chain 'C' and resid 459 through 468 removed outlier: 3.732A pdb=" N ASP C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 614 Processing helix chain 'C' and resid 633 through 647 Processing helix chain 'C' and resid 695 through 702 Processing helix chain 'C' and resid 710 through 723 Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 755 through 761 Processing helix chain 'C' and resid 762 through 776 Processing helix chain 'C' and resid 804 through 823 Proline residue: C 810 - end of helix Processing helix chain 'C' and resid 839 through 841 No H-bonds generated for 'chain 'C' and resid 839 through 841' Processing helix chain 'C' and resid 842 through 852 removed outlier: 3.615A pdb=" N ARG C 852 " --> pdb=" O THR C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 891 Processing helix chain 'C' and resid 928 through 942 Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.775A pdb=" N GLU D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 49 Processing helix chain 'D' and resid 50 through 54 removed outlier: 4.511A pdb=" N ASN D 54 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 108 through 126 Processing helix chain 'I' and resid 16 through 21 removed outlier: 3.715A pdb=" N LEU I 20 " --> pdb=" O PRO I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 31 Processing helix chain 'I' and resid 32 through 39 Processing helix chain 'I' and resid 43 through 53 removed outlier: 4.087A pdb=" N GLU I 53 " --> pdb=" O ASP I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 80 Processing helix chain 'I' and resid 83 through 93 Processing helix chain 'I' and resid 96 through 111 removed outlier: 3.702A pdb=" N ARG I 100 " --> pdb=" O PHE I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 119 removed outlier: 3.720A pdb=" N TYR I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 126 removed outlier: 3.703A pdb=" N ASN I 125 " --> pdb=" O PRO I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 154 Processing helix chain 'I' and resid 167 through 174 Processing helix chain 'K' and resid 271 through 300 removed outlier: 3.552A pdb=" N LEU K 297 " --> pdb=" O ASP K 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 32 Processing helix chain 'M' and resid 38 through 49 Processing helix chain 'M' and resid 62 through 66 Processing helix chain 'M' and resid 67 through 77 removed outlier: 4.214A pdb=" N LEU M 71 " --> pdb=" O LEU M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 112 through 125 Processing helix chain 'U' and resid 112 through 116 removed outlier: 3.536A pdb=" N VAL U 115 " --> pdb=" O ASN U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 150 through 160 Processing helix chain 'U' and resid 186 through 194 removed outlier: 3.631A pdb=" N THR U 190 " --> pdb=" O LEU U 186 " (cutoff:3.500A) Processing helix chain 'U' and resid 198 through 204 Processing helix chain 'U' and resid 205 through 207 No H-bonds generated for 'chain 'U' and resid 205 through 207' Processing helix chain 'U' and resid 233 through 245 Processing helix chain 'U' and resid 246 through 255 removed outlier: 3.812A pdb=" N GLU U 255 " --> pdb=" O ASN U 251 " (cutoff:3.500A) Processing helix chain 'U' and resid 256 through 261 removed outlier: 4.607A pdb=" N ASN U 261 " --> pdb=" O ASP U 257 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 285 removed outlier: 3.892A pdb=" N PHE U 277 " --> pdb=" O LEU U 273 " (cutoff:3.500A) Processing helix chain 'U' and resid 296 through 307 Processing helix chain 'U' and resid 318 through 335 Processing helix chain 'U' and resid 343 through 349 Processing helix chain 'U' and resid 366 through 376 removed outlier: 3.536A pdb=" N HIS U 375 " --> pdb=" O GLU U 371 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN U 376 " --> pdb=" O GLN U 372 " (cutoff:3.500A) Processing helix chain 'U' and resid 377 through 379 No H-bonds generated for 'chain 'U' and resid 377 through 379' Processing helix chain 'U' and resid 415 through 419 Processing helix chain 'U' and resid 538 through 543 removed outlier: 3.983A pdb=" N ILE U 542 " --> pdb=" O LEU U 538 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR U 543 " --> pdb=" O PRO U 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 538 through 543' Processing helix chain 'X' and resid 23 through 33 Processing helix chain 'X' and resid 33 through 82 Processing helix chain 'r' and resid 91 through 100 Processing helix chain 'r' and resid 101 through 108 Processing helix chain 'r' and resid 118 through 133 removed outlier: 3.575A pdb=" N MET r 133 " --> pdb=" O ASN r 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 441 through 466 Processing helix chain 'J' and resid 480 through 485 Processing helix chain 'J' and resid 485 through 492 removed outlier: 3.793A pdb=" N GLN J 491 " --> pdb=" O THR J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 518 Processing helix chain 'J' and resid 521 through 533 Processing helix chain 'J' and resid 553 through 567 Processing helix chain 'J' and resid 587 through 601 Processing helix chain 'J' and resid 653 through 664 removed outlier: 3.588A pdb=" N ALA J 657 " --> pdb=" O THR J 653 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS J 664 " --> pdb=" O HIS J 660 " (cutoff:3.500A) Processing helix chain 'J' and resid 666 through 683 removed outlier: 4.125A pdb=" N TRP J 670 " --> pdb=" O ALA J 666 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 80 removed outlier: 3.728A pdb=" N MET L 59 " --> pdb=" O TRP L 55 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE L 60 " --> pdb=" O ASP L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 119 removed outlier: 3.714A pdb=" N VAL L 92 " --> pdb=" O PRO L 88 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL L 101 " --> pdb=" O ASN L 97 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE L 109 " --> pdb=" O ASN L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 121 No H-bonds generated for 'chain 'L' and resid 120 through 121' Processing helix chain 'L' and resid 122 through 123 No H-bonds generated for 'chain 'L' and resid 122 through 123' Processing helix chain 'L' and resid 124 through 129 Processing helix chain 'L' and resid 131 through 143 Processing helix chain 'L' and resid 149 through 153 removed outlier: 3.681A pdb=" N ASN L 152 " --> pdb=" O CYS L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 159 Processing helix chain 'L' and resid 160 through 173 removed outlier: 3.834A pdb=" N THR L 173 " --> pdb=" O VAL L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 211 Processing helix chain 'L' and resid 211 through 216 removed outlier: 3.575A pdb=" N ILE L 215 " --> pdb=" O ARG L 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA L 216 " --> pdb=" O MET L 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 211 through 216' Processing helix chain 'L' and resid 216 through 236 removed outlier: 3.656A pdb=" N ILE L 221 " --> pdb=" O PRO L 217 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE L 222 " --> pdb=" O ASN L 218 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE L 223 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ALA L 225 " --> pdb=" O ILE L 221 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N SER L 226 " --> pdb=" O ILE L 222 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR L 227 " --> pdb=" O ILE L 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 243 Processing helix chain 'L' and resid 245 through 251 removed outlier: 3.591A pdb=" N LEU L 251 " --> pdb=" O CYS L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 282 Processing helix chain 'L' and resid 284 through 286 No H-bonds generated for 'chain 'L' and resid 284 through 286' Processing helix chain 'L' and resid 287 through 308 removed outlier: 3.859A pdb=" N PHE L 308 " --> pdb=" O ARG L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 332 Processing helix chain 'L' and resid 356 through 367 Processing helix chain 'L' and resid 369 through 376 Processing helix chain 'L' and resid 413 through 417 Processing helix chain 'L' and resid 421 through 432 Processing helix chain 'F' and resid 89 through 99 removed outlier: 3.519A pdb=" N GLN F 98 " --> pdb=" O LYS F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 115 Processing helix chain 'F' and resid 125 through 140 Processing helix chain 'F' and resid 173 through 202 Proline residue: F 187 - end of helix Processing helix chain 'F' and resid 203 through 220 removed outlier: 3.520A pdb=" N SER F 220 " --> pdb=" O LYS F 216 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 113 Processing helix chain 'N' and resid 116 through 135 removed outlier: 3.592A pdb=" N GLU N 129 " --> pdb=" O LYS N 125 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS N 130 " --> pdb=" O GLU N 126 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU N 134 " --> pdb=" O LYS N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 142 removed outlier: 3.517A pdb=" N PHE N 142 " --> pdb=" O ILE N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 148 Processing helix chain 'N' and resid 149 through 152 Processing helix chain 'N' and resid 153 through 159 Processing helix chain 'N' and resid 168 through 173 Processing helix chain 'N' and resid 183 through 194 removed outlier: 4.185A pdb=" N PHE N 187 " --> pdb=" O PRO N 183 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY N 194 " --> pdb=" O HIS N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 290 through 305 Processing helix chain 'N' and resid 308 through 323 removed outlier: 3.597A pdb=" N TRP N 312 " --> pdb=" O HIS N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 339 Processing helix chain 'N' and resid 342 through 353 removed outlier: 3.796A pdb=" N TRP N 346 " --> pdb=" O SER N 342 " (cutoff:3.500A) Processing helix chain 'N' and resid 355 through 369 removed outlier: 4.067A pdb=" N LYS N 359 " --> pdb=" O GLY N 355 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA N 360 " --> pdb=" O ASP N 356 " (cutoff:3.500A) Processing helix chain 'N' and resid 372 through 383 Processing helix chain 'N' and resid 385 through 398 Processing helix chain 'N' and resid 403 through 412 removed outlier: 4.120A pdb=" N TRP N 407 " --> pdb=" O SER N 403 " (cutoff:3.500A) Processing helix chain 'N' and resid 415 through 430 Processing helix chain 'N' and resid 433 through 443 Processing helix chain 'N' and resid 449 through 460 Processing helix chain 'N' and resid 463 through 477 removed outlier: 4.321A pdb=" N TRP N 467 " --> pdb=" O ASP N 463 " (cutoff:3.500A) Processing helix chain 'N' and resid 479 through 498 Processing helix chain 'N' and resid 502 through 516 removed outlier: 4.033A pdb=" N TRP N 506 " --> pdb=" O ASN N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 518 through 532 Processing helix chain 'N' and resid 540 through 553 Processing helix chain 'N' and resid 558 through 569 Processing helix chain 'N' and resid 574 through 587 removed outlier: 3.646A pdb=" N LEU N 578 " --> pdb=" O LYS N 574 " (cutoff:3.500A) Processing helix chain 'N' and resid 589 through 604 Processing helix chain 'N' and resid 607 through 621 removed outlier: 4.027A pdb=" N TRP N 611 " --> pdb=" O ALA N 607 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU N 612 " --> pdb=" O GLU N 608 " (cutoff:3.500A) Processing helix chain 'N' and resid 623 through 637 removed outlier: 3.548A pdb=" N ALA N 637 " --> pdb=" O LEU N 633 " (cutoff:3.500A) Processing helix chain 'N' and resid 643 through 654 removed outlier: 3.613A pdb=" N GLU N 654 " --> pdb=" O LYS N 650 " (cutoff:3.500A) Processing helix chain 'N' and resid 659 through 671 Processing helix chain 'N' and resid 674 through 688 Processing helix chain 'N' and resid 690 through 705 removed outlier: 3.633A pdb=" N LEU N 697 " --> pdb=" O ALA N 693 " (cutoff:3.500A) Processing helix chain 'N' and resid 708 through 722 removed outlier: 3.759A pdb=" N TRP N 712 " --> pdb=" O PHE N 708 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS N 722 " --> pdb=" O ILE N 718 " (cutoff:3.500A) Processing helix chain 'N' and resid 725 through 739 Processing helix chain 'N' and resid 742 through 757 Processing helix chain 'N' and resid 758 through 773 Processing helix chain 'N' and resid 776 through 790 removed outlier: 3.552A pdb=" N GLU N 787 " --> pdb=" O SER N 783 " (cutoff:3.500A) Processing helix chain 'N' and resid 792 through 806 Processing helix chain 'N' and resid 810 through 821 removed outlier: 3.802A pdb=" N PHE N 819 " --> pdb=" O SER N 815 " (cutoff:3.500A) Processing helix chain 'N' and resid 826 through 838 removed outlier: 3.628A pdb=" N VAL N 831 " --> pdb=" O ARG N 827 " (cutoff:3.500A) Processing helix chain 'N' and resid 840 through 854 Processing helix chain 'N' and resid 856 through 870 Processing helix chain 'N' and resid 876 through 888 Processing helix chain 'N' and resid 891 through 904 removed outlier: 3.526A pdb=" N GLU N 895 " --> pdb=" O GLU N 891 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG N 898 " --> pdb=" O GLN N 894 " (cutoff:3.500A) Processing helix chain 'N' and resid 909 through 920 removed outlier: 3.506A pdb=" N ALA N 914 " --> pdb=" O GLU N 910 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS N 917 " --> pdb=" O CYS N 913 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP N 918 " --> pdb=" O ALA N 914 " (cutoff:3.500A) Processing helix chain 'N' and resid 924 through 928 removed outlier: 3.704A pdb=" N ASP N 928 " --> pdb=" O LYS N 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 72 removed outlier: 4.141A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 91 removed outlier: 3.888A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 200 through 205 removed outlier: 4.630A pdb=" N ASP A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 316 through 321 removed outlier: 3.644A pdb=" N ASN A 321 " --> pdb=" O PRO A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.890A pdb=" N TRP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.673A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.750A pdb=" N TYR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 460 Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 489 through 509 Processing helix chain 'A' and resid 531 through 538 Processing helix chain 'A' and resid 541 through 566 Processing helix chain 'A' and resid 570 through 584 Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 590 through 595 removed outlier: 3.938A pdb=" N TYR A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 617 removed outlier: 4.153A pdb=" N GLN A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 657 removed outlier: 3.773A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 677 through 696 removed outlier: 6.875A pdb=" N ASP A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET A 696 " --> pdb=" O ASP A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 700 No H-bonds generated for 'chain 'A' and resid 698 through 700' Processing helix chain 'A' and resid 701 through 722 removed outlier: 6.094A pdb=" N ARG A 707 " --> pdb=" O GLN A 703 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N THR A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 764 Processing helix chain 'A' and resid 768 through 798 Processing helix chain 'A' and resid 802 through 820 Processing helix chain 'A' and resid 834 through 848 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 873 through 888 Processing helix chain 'A' and resid 912 through 933 removed outlier: 3.765A pdb=" N THR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 962 Processing helix chain 'A' and resid 989 through 998 Processing helix chain 'A' and resid 1002 through 1013 removed outlier: 3.611A pdb=" N ASN A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1063 removed outlier: 6.575A pdb=" N LEU A1055 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N HIS A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A1057 " --> pdb=" O LEU A1053 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1081 removed outlier: 3.668A pdb=" N GLU A1080 " --> pdb=" O ASP A1076 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A1081 " --> pdb=" O ILE A1077 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1076 through 1081' Processing helix chain 'A' and resid 1102 through 1117 removed outlier: 3.639A pdb=" N GLU A1116 " --> pdb=" O ARG A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1160 removed outlier: 3.584A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1250 Processing helix chain 'A' and resid 1255 through 1274 removed outlier: 3.612A pdb=" N TYR A1273 " --> pdb=" O GLY A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1304 Processing helix chain 'A' and resid 1313 through 1318 Processing helix chain 'A' and resid 1319 through 1323 Processing helix chain 'A' and resid 1336 through 1339 Processing helix chain 'A' and resid 1367 through 1372 Processing helix chain 'A' and resid 1374 through 1399 Processing helix chain 'A' and resid 1418 through 1424 Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1435 through 1443 Processing helix chain 'A' and resid 1444 through 1446 No H-bonds generated for 'chain 'A' and resid 1444 through 1446' Processing helix chain 'A' and resid 1467 through 1479 Processing helix chain 'A' and resid 1479 through 1487 removed outlier: 4.128A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1494 Processing helix chain 'A' and resid 1507 through 1514 Processing helix chain 'A' and resid 1519 through 1527 Processing helix chain 'A' and resid 1528 through 1538 Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1566 through 1577 removed outlier: 4.031A pdb=" N SER A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1600 removed outlier: 3.563A pdb=" N GLU A1600 " --> pdb=" O VAL A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1688 Processing helix chain 'A' and resid 1721 through 1736 removed outlier: 4.139A pdb=" N GLN A1728 " --> pdb=" O PRO A1724 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'A' and resid 1768 through 1772 Processing helix chain 'A' and resid 1823 through 1828 Processing helix chain 'A' and resid 1832 through 1852 Processing helix chain 'A' and resid 1853 through 1857 Processing helix chain 'A' and resid 1865 through 1867 No H-bonds generated for 'chain 'A' and resid 1865 through 1867' Processing helix chain 'A' and resid 1868 through 1876 Processing helix chain 'A' and resid 1891 through 1898 removed outlier: 4.438A pdb=" N GLN A1894 " --> pdb=" O LEU A1891 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A1895 " --> pdb=" O PRO A1892 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS A1896 " --> pdb=" O PHE A1893 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A1897 " --> pdb=" O GLN A1894 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1909 removed outlier: 3.793A pdb=" N LEU A1905 " --> pdb=" O LYS A1901 " (cutoff:3.500A) Processing helix chain 'A' and resid 1928 through 1946 Processing helix chain 'A' and resid 1946 through 1955 Processing helix chain 'A' and resid 1972 through 1996 removed outlier: 3.733A pdb=" N ILE A1977 " --> pdb=" O ASP A1973 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A1978 " --> pdb=" O GLU A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2012 Processing helix chain 'A' and resid 2020 through 2031 Processing helix chain 'A' and resid 2072 through 2081 removed outlier: 3.771A pdb=" N ILE A2078 " --> pdb=" O ARG A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2084 through 2089 removed outlier: 4.183A pdb=" N HIS A2089 " --> pdb=" O LEU A2085 " (cutoff:3.500A) Processing helix chain 'A' and resid 2107 through 2118 removed outlier: 3.526A pdb=" N LEU A2111 " --> pdb=" O PRO A2107 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2202 Processing helix chain 'A' and resid 2231 through 2241 Processing helix chain 'A' and resid 2252 through 2254 No H-bonds generated for 'chain 'A' and resid 2252 through 2254' Processing helix chain 'A' and resid 2310 through 2317 removed outlier: 3.983A pdb=" N PHE A2314 " --> pdb=" O ARG A2310 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A2317 " --> pdb=" O HIS A2313 " (cutoff:3.500A) Processing helix chain 'S' and resid 157 through 185 removed outlier: 3.635A pdb=" N ARG S 162 " --> pdb=" O PRO S 158 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN S 182 " --> pdb=" O ARG S 178 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS S 183 " --> pdb=" O LEU S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 200 through 219 removed outlier: 3.744A pdb=" N LYS S 219 " --> pdb=" O ASP S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 262 through 266 Processing helix chain 'S' and resid 291 through 309 Processing helix chain 'S' and resid 328 through 330 No H-bonds generated for 'chain 'S' and resid 328 through 330' Processing helix chain 'S' and resid 331 through 336 removed outlier: 3.704A pdb=" N SER S 335 " --> pdb=" O ARG S 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '7' and resid 410 through 412 Processing sheet with id=AA2, first strand: chain 'C' and resid 184 through 188 removed outlier: 6.266A pdb=" N ARG C 130 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N MET C 203 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL C 132 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N GLY C 224 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN C 131 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL C 226 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR C 133 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N PHE C 228 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS C 135 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ASP C 230 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N CYS C 308 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 255 " --> pdb=" O CYS C 308 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N SER C 310 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE C 257 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 348 through 350 removed outlier: 3.546A pdb=" N LYS C 355 " --> pdb=" O ASN C 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 523 through 526 removed outlier: 5.245A pdb=" N THR C 478 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ARG C 495 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 494 " --> pdb=" O VAL C 550 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TRP C 549 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER C 533 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 501 through 502 Processing sheet with id=AA6, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.750A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.750A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 783 through 784 removed outlier: 6.611A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 783 through 784 removed outlier: 3.524A pdb=" N HIS C 903 " --> pdb=" O TYR C 831 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N PHE C 833 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N PHE C 901 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLU C 835 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N SER C 899 " --> pdb=" O GLU C 835 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLN C 837 " --> pdb=" O SER C 897 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N SER C 897 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 674 through 677 removed outlier: 6.346A pdb=" N LYS C 684 " --> pdb=" O ALA C 794 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA C 794 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASN C 743 " --> pdb=" O PHE C 735 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE C 735 " --> pdb=" O ASN C 743 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU C 745 " --> pdb=" O TRP C 733 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 7 through 8 removed outlier: 4.532A pdb=" N ASP D 62 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL D 25 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N TYR D 59 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL D 27 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL D 61 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG D 29 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 91 through 93 Processing sheet with id=AB4, first strand: chain 'I' and resid 60 through 61 Processing sheet with id=AB5, first strand: chain 'I' and resid 129 through 133 Processing sheet with id=AB6, first strand: chain 'I' and resid 156 through 157 Processing sheet with id=AB7, first strand: chain 'M' and resid 35 through 37 removed outlier: 6.569A pdb=" N CYS M 102 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE M 54 " --> pdb=" O CYS M 102 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL M 104 " --> pdb=" O GLU M 52 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N VAL M 81 " --> pdb=" O GLU M 52 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE M 54 " --> pdb=" O VAL M 81 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL M 83 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N MET M 56 " --> pdb=" O VAL M 83 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 142 through 143 removed outlier: 3.669A pdb=" N LYS U 171 " --> pdb=" O ASN U 166 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE U 172 " --> pdb=" O ILE U 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 226 through 227 removed outlier: 6.535A pdb=" N GLY U 226 " --> pdb=" O VAL U 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'U' and resid 381 through 388 removed outlier: 6.330A pdb=" N SER U 352 " --> pdb=" O THR U 444 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS U 428 " --> pdb=" O LYS U 439 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 391 through 393 removed outlier: 6.324A pdb=" N LEU U 391 " --> pdb=" O CYS U 453 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR U 548 " --> pdb=" O ILE U 454 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ALA U 547 " --> pdb=" O HIS U 505 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS U 505 " --> pdb=" O ALA U 547 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA U 501 " --> pdb=" O ILE U 551 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS U 553 " --> pdb=" O LEU U 499 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU U 499 " --> pdb=" O LYS U 553 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL U 478 " --> pdb=" O TYR U 497 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 391 through 393 removed outlier: 6.324A pdb=" N LEU U 391 " --> pdb=" O CYS U 453 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR U 548 " --> pdb=" O ILE U 454 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ALA U 547 " --> pdb=" O HIS U 505 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS U 505 " --> pdb=" O ALA U 547 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA U 501 " --> pdb=" O ILE U 551 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS U 553 " --> pdb=" O LEU U 499 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU U 499 " --> pdb=" O LYS U 553 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE U 500 " --> pdb=" O LEU U 519 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP U 526 " --> pdb=" O ILE U 537 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'U' and resid 412 through 414 removed outlier: 6.642A pdb=" N VAL U 413 " --> pdb=" O ASN U 472 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'U' and resid 457 through 459 Processing sheet with id=AC6, first strand: chain 'X' and resid 10 through 13 Processing sheet with id=AC7, first strand: chain 'r' and resid 47 through 49 removed outlier: 6.270A pdb=" N GLU r 47 " --> pdb=" O SER r 111 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG r 113 " --> pdb=" O GLU r 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'r' and resid 65 through 67 Processing sheet with id=AC9, first strand: chain 'r' and resid 80 through 82 Processing sheet with id=AD1, first strand: chain 'J' and resid 630 through 638 removed outlier: 5.452A pdb=" N LEU J 632 " --> pdb=" O ARG J 547 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG J 547 " --> pdb=" O LEU J 632 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 377 through 379 Processing sheet with id=AD3, first strand: chain 'F' and resid 221 through 228 removed outlier: 3.655A pdb=" N MET F 520 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU F 518 " --> pdb=" O PHE F 224 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER F 226 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE F 516 " --> pdb=" O SER F 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY F 497 " --> pdb=" O CYS F 510 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 234 through 239 removed outlier: 7.035A pdb=" N CYS F 255 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR F 268 " --> pdb=" O CYS F 255 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU F 257 " --> pdb=" O LEU F 266 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 276 through 281 removed outlier: 6.489A pdb=" N CYS F 299 " --> pdb=" O GLY F 277 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE F 279 " --> pdb=" O ALA F 297 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA F 297 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA F 317 " --> pdb=" O LEU F 307 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 326 through 331 removed outlier: 4.210A pdb=" N ARG F 328 " --> pdb=" O THR F 341 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER F 346 " --> pdb=" O CYS F 342 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TRP F 347 " --> pdb=" O HIS F 360 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N HIS F 360 " --> pdb=" O TRP F 347 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU F 349 " --> pdb=" O ILE F 358 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 368 through 373 removed outlier: 3.613A pdb=" N MET F 401 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP F 393 " --> pdb=" O CYS F 399 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N CYS F 399 " --> pdb=" O ASP F 393 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 410 through 415 removed outlier: 6.292A pdb=" N GLY F 425 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE F 413 " --> pdb=" O ALA F 423 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA F 423 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE F 415 " --> pdb=" O HIS F 421 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N HIS F 421 " --> pdb=" O PHE F 415 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ASP F 435 " --> pdb=" O CYS F 441 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N CYS F 441 " --> pdb=" O ASP F 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 452 through 457 removed outlier: 3.606A pdb=" N ALA F 469 " --> pdb=" O THR F 473 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR F 473 " --> pdb=" O ALA F 469 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA F 474 " --> pdb=" O LEU F 488 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS F 486 " --> pdb=" O ILE F 476 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N THR F 478 " --> pdb=" O PRO F 484 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 199 through 200 removed outlier: 3.972A pdb=" N LEU A1403 " --> pdb=" O VAL N 200 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 253 through 254 Processing sheet with id=AE3, first strand: chain 'N' and resid 269 through 271 removed outlier: 4.463A pdb=" N MET A1914 " --> pdb=" O LYS N 271 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A1913 " --> pdb=" O ILE A1821 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TRP A1778 " --> pdb=" O ILE A1862 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A1887 " --> pdb=" O VAL A1863 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AE5, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AE6, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AE7, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AE8, first strand: chain 'A' and resid 905 through 910 removed outlier: 6.237A pdb=" N VAL A 894 " --> pdb=" O ASN A1018 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 1085 through 1090 removed outlier: 3.609A pdb=" N VAL A 975 " --> pdb=" O PHE A1099 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 1185 through 1189 removed outlier: 7.291A pdb=" N LEU A1216 " --> pdb=" O THR A1225 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN A1227 " --> pdb=" O TRP A1214 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TRP A1214 " --> pdb=" O GLN A1227 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 1334 through 1335 removed outlier: 3.713A pdb=" N GLN A1363 " --> pdb=" O ILE A1335 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 1341 through 1345 Processing sheet with id=AF4, first strand: chain 'A' and resid 1553 through 1554 Processing sheet with id=AF5, first strand: chain 'A' and resid 1606 through 1611 removed outlier: 8.400A pdb=" N ILE A1606 " --> pdb=" O SER A1634 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N SER A1634 " --> pdb=" O ILE A1606 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A1608 " --> pdb=" O PHE A1632 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN A1658 " --> pdb=" O ALA A1633 " (cutoff:3.500A) removed outlier: 11.408A pdb=" N TYR A1635 " --> pdb=" O THR A1656 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N THR A1656 " --> pdb=" O TYR A1635 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N VAL A1701 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 1798 through 1803 removed outlier: 4.416A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR S 258 " --> pdb=" O LEU S 289 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 2090 through 2091 removed outlier: 6.126A pdb=" N TYR A2091 " --> pdb=" O LEU A2225 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ALA A2227 " --> pdb=" O TYR A2091 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TRP A2177 " --> pdb=" O ILE A2214 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N CYS A2216 " --> pdb=" O TRP A2177 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HIS A2179 " --> pdb=" O CYS A2216 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 2090 through 2091 removed outlier: 6.126A pdb=" N TYR A2091 " --> pdb=" O LEU A2225 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ALA A2227 " --> pdb=" O TYR A2091 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA A2227 " --> pdb=" O VAL A2259 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 2104 through 2106 Processing sheet with id=AG1, first strand: chain 'A' and resid 2272 through 2274 2462 hydrogen bonds defined for protein. 7122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 135 hydrogen bonds 234 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 131 stacking parallelities Total time for adding SS restraints: 38.46 Time building geometry restraints manager: 13.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14130 1.33 - 1.45: 11517 1.45 - 1.57: 29757 1.57 - 1.69: 474 1.69 - 1.82: 357 Bond restraints: 56235 Sorted by residual: bond pdb=" O12 IHP A2401 " pdb=" P2 IHP A2401 " ideal model delta sigma weight residual 1.675 1.609 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O16 IHP A2401 " pdb=" P6 IHP A2401 " ideal model delta sigma weight residual 1.672 1.606 0.066 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O14 IHP A2401 " pdb=" P4 IHP A2401 " ideal model delta sigma weight residual 1.671 1.606 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O15 IHP A2401 " pdb=" P5 IHP A2401 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O13 IHP A2401 " pdb=" P3 IHP A2401 " ideal model delta sigma weight residual 1.669 1.608 0.061 2.00e-02 2.50e+03 9.21e+00 ... (remaining 56230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 76240 1.64 - 3.27: 886 3.27 - 4.91: 128 4.91 - 6.54: 46 6.54 - 8.18: 9 Bond angle restraints: 77309 Sorted by residual: angle pdb=" N ILE N 534 " pdb=" CA ILE N 534 " pdb=" C ILE N 534 " ideal model delta sigma weight residual 113.20 108.92 4.28 9.60e-01 1.09e+00 1.99e+01 angle pdb=" CA PRO C 800 " pdb=" N PRO C 800 " pdb=" CD PRO C 800 " ideal model delta sigma weight residual 112.00 106.32 5.68 1.40e+00 5.10e-01 1.64e+01 angle pdb=" N GLN F 212 " pdb=" CA GLN F 212 " pdb=" CB GLN F 212 " ideal model delta sigma weight residual 110.28 116.41 -6.13 1.55e+00 4.16e-01 1.56e+01 angle pdb=" N ILE U 500 " pdb=" CA ILE U 500 " pdb=" C ILE U 500 " ideal model delta sigma weight residual 113.53 109.77 3.76 9.80e-01 1.04e+00 1.47e+01 angle pdb=" C3' U 5 78 " pdb=" O3' U 5 78 " pdb=" P C 5 79 " ideal model delta sigma weight residual 120.20 125.14 -4.94 1.50e+00 4.44e-01 1.08e+01 ... (remaining 77304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 33431 35.61 - 71.21: 893 71.21 - 106.82: 83 106.82 - 142.43: 7 142.43 - 178.04: 9 Dihedral angle restraints: 34423 sinusoidal: 16106 harmonic: 18317 Sorted by residual: dihedral pdb=" O4' Uz1 6 " pdb=" C1' Uz1 6 " pdb=" N1 Uz1 6 " pdb=" C2 Uz1 6 " ideal model delta sinusoidal sigma weight residual 200.00 30.86 169.14 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' U 5 78 " pdb=" C1' U 5 78 " pdb=" N1 U 5 78 " pdb=" C2 U 5 78 " ideal model delta sinusoidal sigma weight residual -128.00 50.04 -178.04 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 5 80 " pdb=" C1' U 5 80 " pdb=" N1 U 5 80 " pdb=" C2 U 5 80 " ideal model delta sinusoidal sigma weight residual -128.00 49.50 -177.50 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 34420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.998: 8785 0.998 - 1.996: 0 1.996 - 2.994: 0 2.994 - 3.992: 0 3.992 - 4.990: 4 Chirality restraints: 8789 Sorted by residual: chirality pdb=" C2 IHP A2401 " pdb=" C1 IHP A2401 " pdb=" C3 IHP A2401 " pdb=" O12 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.52 2.47 -4.99 2.00e-01 2.50e+01 6.22e+02 chirality pdb=" C5 IHP A2401 " pdb=" C4 IHP A2401 " pdb=" C6 IHP A2401 " pdb=" O15 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.42 2.46 -4.88 2.00e-01 2.50e+01 5.95e+02 chirality pdb=" C1 IHP A2401 " pdb=" C2 IHP A2401 " pdb=" C6 IHP A2401 " pdb=" O11 IHP A2401 " both_signs ideal model delta sigma weight residual False 2.32 -2.41 4.73 2.00e-01 2.50e+01 5.58e+02 ... (remaining 8786 not shown) Planarity restraints: 9073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 799 " -0.045 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO C 800 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 800 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 800 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL U 246 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO U 247 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO U 247 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO U 247 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 947 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A 948 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 948 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 948 " 0.020 5.00e-02 4.00e+02 ... (remaining 9070 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4707 2.74 - 3.28: 54266 3.28 - 3.82: 97307 3.82 - 4.36: 116285 4.36 - 4.90: 190239 Nonbonded interactions: 462804 Sorted by model distance: nonbonded pdb=" OD2 ASP A1146 " pdb=" ND2 ASN A1182 " model vdw 2.202 3.120 nonbonded pdb=" OG1 THR A1102 " pdb=" OD1 ASP A1104 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR A1091 " pdb=" OD2 ASP A1441 " model vdw 2.206 3.040 nonbonded pdb=" OG SER F 259 " pdb=" O ASP F 262 " model vdw 2.211 3.040 nonbonded pdb=" OE1 GLN I 18 " pdb=" OH TYR I 30 " model vdw 2.222 3.040 ... (remaining 462799 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.930 Check model and map are aligned: 0.330 Set scattering table: 0.450 Process input model: 134.090 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.002 0.114 56235 Z= 0.164 Angle : 0.471 8.180 77309 Z= 0.245 Chirality : 0.109 4.990 8789 Planarity : 0.003 0.065 9073 Dihedral : 15.699 178.037 22531 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.39 (0.11), residues: 6199 helix: 1.94 (0.10), residues: 2837 sheet: 0.10 (0.19), residues: 761 loop : 0.12 (0.13), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1263 HIS 0.005 0.001 HIS A1674 PHE 0.018 0.001 PHE J 643 TYR 0.021 0.001 TYR A1044 ARG 0.004 0.000 ARG A1787 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 5.333 Fit side-chains revert: symmetry clash REVERT: r 57 ASP cc_start: 0.7155 (p0) cc_final: 0.6892 (p0) REVERT: J 536 ASP cc_start: 0.6648 (p0) cc_final: 0.6438 (p0) REVERT: N 679 MET cc_start: 0.7255 (ppp) cc_final: 0.6816 (ppp) REVERT: A 2033 THR cc_start: 0.7530 (m) cc_final: 0.7294 (p) REVERT: S 356 THR cc_start: 0.8067 (p) cc_final: 0.7847 (p) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.5046 time to fit residues: 201.7588 Evaluate side-chains 195 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 4.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 641 random chunks: chunk 541 optimal weight: 2.9990 chunk 485 optimal weight: 1.9990 chunk 269 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 327 optimal weight: 5.9990 chunk 259 optimal weight: 0.7980 chunk 502 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 chunk 373 optimal weight: 7.9990 chunk 582 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 HIS ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 407 GLN U 530 GLN X 39 ASN r 107 ASN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 508 GLN J 515 ASN ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 376 ASN ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 HIS ** F 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 792 HIS ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2255 HIS ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 211 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 56235 Z= 0.222 Angle : 0.541 14.424 77309 Z= 0.273 Chirality : 0.043 0.902 8789 Planarity : 0.004 0.053 9073 Dihedral : 15.756 179.304 10467 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.23 % Allowed : 4.23 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.34 (0.11), residues: 6199 helix: 1.92 (0.10), residues: 2914 sheet: -0.03 (0.19), residues: 768 loop : 0.07 (0.13), residues: 2517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 637 HIS 0.006 0.001 HIS r 98 PHE 0.022 0.001 PHE J 594 TYR 0.014 0.001 TYR A 431 ARG 0.006 0.000 ARG A1195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 200 time to evaluate : 4.881 Fit side-chains revert: symmetry clash REVERT: C 687 MET cc_start: 0.8409 (ttp) cc_final: 0.8149 (ttm) REVERT: r 57 ASP cc_start: 0.7137 (p0) cc_final: 0.6820 (p0) REVERT: J 536 ASP cc_start: 0.6748 (p0) cc_final: 0.6511 (p0) REVERT: N 679 MET cc_start: 0.7415 (ppp) cc_final: 0.6904 (ppp) REVERT: A 1237 MET cc_start: 0.8203 (mtt) cc_final: 0.7955 (mtm) outliers start: 12 outliers final: 5 residues processed: 207 average time/residue: 0.5160 time to fit residues: 193.4381 Evaluate side-chains 197 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 192 time to evaluate : 4.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 211 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 641 random chunks: chunk 323 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 484 optimal weight: 0.8980 chunk 396 optimal weight: 0.5980 chunk 160 optimal weight: 0.4980 chunk 583 optimal weight: 0.8980 chunk 629 optimal weight: 1.9990 chunk 519 optimal weight: 3.9990 chunk 578 optimal weight: 0.9980 chunk 198 optimal weight: 0.3980 chunk 467 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN U 166 ASN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 308 HIS ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1710 ASN A2255 HIS A2309 HIS S 211 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 56235 Z= 0.144 Angle : 0.481 8.644 77309 Z= 0.245 Chirality : 0.039 0.499 8789 Planarity : 0.004 0.050 9073 Dihedral : 15.713 178.817 10467 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.50 % Allowed : 5.66 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.42 (0.11), residues: 6199 helix: 2.05 (0.10), residues: 2911 sheet: -0.20 (0.19), residues: 747 loop : 0.08 (0.13), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 637 HIS 0.004 0.001 HIS U 375 PHE 0.012 0.001 PHE A1719 TYR 0.011 0.001 TYR A1044 ARG 0.007 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 205 time to evaluate : 4.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 687 MET cc_start: 0.8416 (ttp) cc_final: 0.7930 (ttm) REVERT: U 281 MET cc_start: 0.7725 (tpp) cc_final: 0.7426 (tpp) REVERT: r 112 MET cc_start: 0.7818 (mmm) cc_final: 0.7413 (mmm) REVERT: J 536 ASP cc_start: 0.6902 (p0) cc_final: 0.6681 (p0) REVERT: F 401 MET cc_start: 0.8369 (ttt) cc_final: 0.7924 (ttt) REVERT: N 679 MET cc_start: 0.7413 (ppp) cc_final: 0.6885 (ppp) REVERT: A 76 MET cc_start: 0.2800 (mmm) cc_final: 0.2543 (mmp) outliers start: 26 outliers final: 11 residues processed: 222 average time/residue: 0.5101 time to fit residues: 204.2904 Evaluate side-chains 203 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 192 time to evaluate : 5.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1227 GLN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 199 ASP Chi-restraints excluded: chain S residue 211 GLN Chi-restraints excluded: chain S residue 290 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 641 random chunks: chunk 576 optimal weight: 0.1980 chunk 438 optimal weight: 5.9990 chunk 302 optimal weight: 0.0670 chunk 64 optimal weight: 9.9990 chunk 278 optimal weight: 0.9990 chunk 391 optimal weight: 5.9990 chunk 585 optimal weight: 0.0770 chunk 619 optimal weight: 20.0000 chunk 305 optimal weight: 9.9990 chunk 554 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 308 HIS ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2032 GLN A2255 HIS S 211 GLN S 328 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 56235 Z= 0.174 Angle : 0.478 8.397 77309 Z= 0.243 Chirality : 0.039 0.473 8789 Planarity : 0.003 0.049 9073 Dihedral : 15.647 178.982 10467 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 7.17 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.44 (0.11), residues: 6199 helix: 2.09 (0.10), residues: 2916 sheet: -0.27 (0.19), residues: 750 loop : 0.09 (0.13), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 750 HIS 0.004 0.001 HIS r 98 PHE 0.013 0.001 PHE J 643 TYR 0.014 0.001 TYR N 732 ARG 0.004 0.000 ARG N 394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 4.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 687 MET cc_start: 0.8438 (ttp) cc_final: 0.7868 (ttm) REVERT: U 281 MET cc_start: 0.7751 (tpp) cc_final: 0.7358 (tpp) REVERT: U 389 MET cc_start: 0.7744 (tpp) cc_final: 0.7235 (tpp) REVERT: J 536 ASP cc_start: 0.6934 (p0) cc_final: 0.6700 (p0) REVERT: F 401 MET cc_start: 0.8241 (ttt) cc_final: 0.7917 (ttt) REVERT: N 679 MET cc_start: 0.7276 (ppp) cc_final: 0.6855 (ppp) REVERT: A 76 MET cc_start: 0.2456 (mmm) cc_final: 0.2247 (mmp) REVERT: S 356 THR cc_start: 0.8048 (p) cc_final: 0.7716 (p) outliers start: 34 outliers final: 17 residues processed: 219 average time/residue: 0.5630 time to fit residues: 224.0551 Evaluate side-chains 210 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 4.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1227 GLN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 2016 ILE Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 199 ASP Chi-restraints excluded: chain S residue 211 GLN Chi-restraints excluded: chain S residue 290 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 641 random chunks: chunk 516 optimal weight: 2.9990 chunk 351 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 461 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 chunk 528 optimal weight: 0.6980 chunk 428 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 316 optimal weight: 2.9990 chunk 556 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 308 HIS ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 56235 Z= 0.193 Angle : 0.480 8.695 77309 Z= 0.244 Chirality : 0.039 0.441 8789 Planarity : 0.003 0.049 9073 Dihedral : 15.629 179.068 10467 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.63 % Allowed : 8.00 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.46 (0.11), residues: 6199 helix: 2.11 (0.10), residues: 2923 sheet: -0.30 (0.19), residues: 751 loop : 0.10 (0.13), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 750 HIS 0.004 0.001 HIS r 98 PHE 0.021 0.001 PHE J 643 TYR 0.011 0.001 TYR A 921 ARG 0.004 0.000 ARG C 645 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 196 time to evaluate : 4.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 687 MET cc_start: 0.8459 (ttp) cc_final: 0.7859 (ttm) REVERT: U 281 MET cc_start: 0.7718 (tpp) cc_final: 0.7355 (tpp) REVERT: U 389 MET cc_start: 0.7709 (tpp) cc_final: 0.7335 (tpp) REVERT: J 536 ASP cc_start: 0.6762 (p0) cc_final: 0.6506 (p0) REVERT: F 401 MET cc_start: 0.8296 (ttt) cc_final: 0.7963 (ttt) REVERT: N 679 MET cc_start: 0.7137 (ppp) cc_final: 0.6871 (ppp) REVERT: A 1327 MET cc_start: 0.8495 (ttt) cc_final: 0.7611 (ttt) REVERT: A 1937 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9109 (mm) REVERT: S 356 THR cc_start: 0.8038 (p) cc_final: 0.7729 (p) outliers start: 33 outliers final: 19 residues processed: 217 average time/residue: 0.4928 time to fit residues: 192.8848 Evaluate side-chains 213 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 4.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain r residue 91 ASP Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1227 GLN Chi-restraints excluded: chain A residue 1295 ILE Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1937 ILE Chi-restraints excluded: chain A residue 2016 ILE Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 290 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 641 random chunks: chunk 208 optimal weight: 3.9990 chunk 557 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 363 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 620 optimal weight: 20.0000 chunk 514 optimal weight: 3.9990 chunk 287 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 325 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 575 GLN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 GLN M 115 GLN r 74 GLN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 307 HIS A1476 GLN ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1710 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 56235 Z= 0.293 Angle : 0.530 9.083 77309 Z= 0.269 Chirality : 0.041 0.486 8789 Planarity : 0.004 0.053 9073 Dihedral : 15.656 179.485 10467 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.86 % Allowed : 8.63 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.35 (0.11), residues: 6199 helix: 2.02 (0.10), residues: 2927 sheet: -0.38 (0.19), residues: 757 loop : 0.06 (0.13), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 312 HIS 0.006 0.001 HIS A1674 PHE 0.016 0.001 PHE J 643 TYR 0.015 0.001 TYR A1091 ARG 0.007 0.000 ARG A1667 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 195 time to evaluate : 4.789 Fit side-chains REVERT: 7 449 LYS cc_start: 0.6840 (pttp) cc_final: 0.5792 (pttm) REVERT: C 687 MET cc_start: 0.8510 (ttp) cc_final: 0.7855 (ttm) REVERT: U 281 MET cc_start: 0.7515 (tpp) cc_final: 0.7235 (tpp) REVERT: U 389 MET cc_start: 0.7576 (tpp) cc_final: 0.7049 (tpp) REVERT: F 401 MET cc_start: 0.8269 (ttt) cc_final: 0.7902 (ttt) REVERT: N 679 MET cc_start: 0.7098 (ppp) cc_final: 0.6808 (ppp) REVERT: N 800 MET cc_start: 0.8888 (tpp) cc_final: 0.8484 (tpp) REVERT: A 1327 MET cc_start: 0.8744 (ttt) cc_final: 0.8207 (ttt) REVERT: A 1937 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9134 (mm) REVERT: S 356 THR cc_start: 0.8156 (p) cc_final: 0.7754 (p) outliers start: 45 outliers final: 26 residues processed: 225 average time/residue: 0.5375 time to fit residues: 218.4937 Evaluate side-chains 219 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 192 time to evaluate : 4.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain r residue 91 ASP Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 980 ARG Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1874 VAL Chi-restraints excluded: chain A residue 1889 LEU Chi-restraints excluded: chain A residue 1937 ILE Chi-restraints excluded: chain A residue 2016 ILE Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 199 ASP Chi-restraints excluded: chain S residue 290 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 56.0921 > 50: distance: 58 - 77: 3.245 distance: 62 - 87: 17.758 distance: 66 - 95: 33.009 distance: 69 - 77: 3.592 distance: 70 - 101: 21.224 distance: 77 - 78: 3.963 distance: 78 - 79: 5.751 distance: 79 - 80: 8.898 distance: 79 - 87: 10.873 distance: 80 - 112: 4.371 distance: 81 - 82: 5.244 distance: 82 - 83: 11.938 distance: 82 - 84: 10.416 distance: 83 - 85: 4.224 distance: 84 - 86: 6.715 distance: 85 - 86: 12.387 distance: 87 - 88: 6.963 distance: 88 - 89: 16.257 distance: 88 - 91: 5.041 distance: 89 - 90: 32.215 distance: 89 - 95: 21.540 distance: 90 - 121: 28.511 distance: 91 - 92: 8.889 distance: 92 - 93: 4.877 distance: 92 - 94: 6.343 distance: 95 - 96: 43.543 distance: 96 - 97: 9.030 distance: 96 - 99: 11.219 distance: 97 - 98: 11.860 distance: 97 - 101: 19.040 distance: 98 - 128: 26.338 distance: 99 - 100: 23.359 distance: 101 - 102: 11.834 distance: 102 - 103: 9.669 distance: 103 - 104: 6.254 distance: 103 - 112: 7.126 distance: 104 - 136: 9.838 distance: 105 - 106: 7.501 distance: 106 - 107: 5.957 distance: 107 - 108: 4.735 distance: 108 - 109: 7.533 distance: 109 - 110: 5.247 distance: 109 - 111: 3.064 distance: 112 - 113: 3.455 distance: 113 - 116: 4.974 distance: 114 - 121: 4.785 distance: 115 - 147: 10.328 distance: 116 - 117: 4.732 distance: 117 - 118: 4.461 distance: 118 - 119: 4.228 distance: 118 - 120: 3.452 distance: 121 - 122: 5.879 distance: 122 - 123: 6.748 distance: 122 - 125: 3.208 distance: 123 - 124: 7.558 distance: 123 - 128: 7.155 distance: 124 - 155: 13.887 distance: 125 - 126: 6.920 distance: 125 - 127: 5.347 distance: 128 - 129: 6.669 distance: 129 - 130: 4.587 distance: 129 - 132: 9.500 distance: 130 - 131: 5.742 distance: 130 - 136: 5.028 distance: 131 - 162: 7.948 distance: 132 - 133: 9.848 distance: 133 - 134: 15.208 distance: 133 - 135: 9.137 distance: 137 - 138: 3.819 distance: 138 - 139: 14.538 distance: 138 - 147: 7.305 distance: 139 - 168: 17.021 distance: 140 - 141: 6.570 distance: 141 - 142: 4.235 distance: 142 - 143: 7.126 distance: 143 - 144: 4.275 distance: 144 - 145: 4.716 distance: 144 - 146: 5.228 distance: 147 - 148: 9.265 distance: 148 - 149: 4.134 distance: 148 - 151: 11.432 distance: 149 - 150: 3.714 distance: 150 - 175: 5.234 distance: 151 - 152: 8.625 distance: 152 - 153: 9.222 distance: 152 - 154: 9.179 distance: 155 - 156: 6.136 distance: 156 - 159: 10.539 distance: 158 - 182: 5.165 distance: 159 - 160: 6.355 distance: 159 - 161: 14.871