Starting phenix.real_space_refine on Mon Jun 24 23:56:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpe_18548/06_2024/8qpe_18548_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpe_18548/06_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_18548/06_2024/8qpe_18548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpe_18548/06_2024/8qpe_18548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpe_18548/06_2024/8qpe_18548_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpe_18548/06_2024/8qpe_18548_updated.pdb" } 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 Residue "7 GLU 418": "OE1" <-> "OE2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "A PHE 1502": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 21.95, per 1000 atoms: 0.40 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.80 Conformation dependent library (CDL) restraints added in 6.6 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... running ksdssp... Secondary structure from input PDB file: 237 helices and 44 sheets defined 44.3% alpha, 10.1% beta 56 base pairs and 131 stacking pairs defined. Time for finding SS restraints: 20.48 Creating SS restraints... Processing helix chain '7' and resid 422 through 432 removed outlier: 3.527A pdb=" N MET 7 425 " --> pdb=" O ALA 7 422 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLN 7 426 " --> pdb=" O SER 7 423 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU 7 427 " --> pdb=" O LYS 7 424 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE 7 431 " --> pdb=" O HIS 7 428 " (cutoff:3.500A) Processing helix chain '7' and resid 436 through 449 Processing helix chain '7' and resid 459 through 472 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 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 142 through 153 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.550A pdb=" N SER C 212 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP C 213 " --> pdb=" O ASN C 210 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG C 220 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 271 through 292 Processing helix chain 'C' and resid 296 through 298 No H-bonds generated for 'chain 'C' and resid 296 through 298' Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.717A pdb=" N LYS C 341 " --> pdb=" O GLN C 337 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 374 through 385 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) Processing helix chain 'C' and resid 392 through 398 Processing helix chain 'C' and resid 412 through 424 Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 441 through 452 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 460 through 467 removed outlier: 3.732A pdb=" N ASP C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 613 Proline residue: C 601 - end of helix Processing helix chain 'C' and resid 634 through 646 Processing helix chain 'C' and resid 696 through 701 Processing helix chain 'C' and resid 711 through 722 Processing helix chain 'C' and resid 726 through 731 removed outlier: 3.683A pdb=" N SER C 731 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 775 removed outlier: 4.381A pdb=" N VAL C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 822 Proline residue: C 810 - end of helix Processing helix chain 'C' and resid 840 through 853 removed outlier: 3.589A pdb=" N VAL C 843 " --> pdb=" O ALA C 840 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER C 844 " --> pdb=" O ASP C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 890 Processing helix chain 'C' and resid 929 through 941 Processing helix chain 'D' and resid 11 through 20 Processing helix chain 'D' and resid 36 through 47 Processing helix chain 'D' and resid 51 through 54 removed outlier: 4.511A pdb=" N ASN D 54 " --> pdb=" O LYS D 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 51 through 54' Processing helix chain 'D' and resid 70 through 73 No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'D' and resid 109 through 125 Processing helix chain 'I' and resid 17 through 20 removed outlier: 3.715A pdb=" N LEU I 20 " --> pdb=" O PRO I 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 17 through 20' Processing helix chain 'I' and resid 23 through 30 Processing helix chain 'I' and resid 33 through 38 Processing helix chain 'I' and resid 44 through 52 Processing helix chain 'I' and resid 69 through 79 Processing helix chain 'I' and resid 84 through 92 Processing helix chain 'I' and resid 97 through 110 Processing helix chain 'I' and resid 113 through 118 removed outlier: 3.720A pdb=" N TYR I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 125 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 153 Processing helix chain 'I' and resid 168 through 174 Processing helix chain 'K' and resid 271 through 299 removed outlier: 3.552A pdb=" N LEU K 297 " --> pdb=" O ASP K 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 31 Processing helix chain 'M' and resid 39 through 48 Processing helix chain 'M' and resid 63 through 65 No H-bonds generated for 'chain 'M' and resid 63 through 65' Processing helix chain 'M' and resid 67 through 76 removed outlier: 4.214A pdb=" N LEU M 71 " --> pdb=" O LEU M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 92 Processing helix chain 'M' and resid 113 through 124 Processing helix chain 'U' and resid 113 through 115 No H-bonds generated for 'chain 'U' and resid 113 through 115' Processing helix chain 'U' and resid 151 through 159 Processing helix chain 'U' and resid 185 through 193 removed outlier: 4.136A pdb=" N ASP U 188 " --> pdb=" O SER U 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 199 through 206 removed outlier: 4.715A pdb=" N ASP U 206 " --> pdb=" O ILE U 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 234 through 244 Processing helix chain 'U' and resid 247 through 254 Processing helix chain 'U' and resid 256 through 260 removed outlier: 3.533A pdb=" N TYR U 259 " --> pdb=" O GLU U 256 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS U 260 " --> pdb=" O ASP U 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 256 through 260' Processing helix chain 'U' and resid 270 through 284 removed outlier: 4.069A pdb=" N GLN U 275 " --> pdb=" O LEU U 272 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG U 276 " --> pdb=" O LEU U 273 " (cutoff:3.500A) Processing helix chain 'U' and resid 297 through 306 Processing helix chain 'U' and resid 319 through 335 Processing helix chain 'U' and resid 344 through 348 Processing helix chain 'U' and resid 367 through 375 removed outlier: 3.536A pdb=" N HIS U 375 " --> pdb=" O GLU U 371 " (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 420 Processing helix chain 'U' and resid 539 through 544 removed outlier: 4.565A pdb=" N THR U 543 " --> pdb=" O PRO U 539 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU U 544 " --> pdb=" O GLN U 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 539 through 544' Processing helix chain 'X' and resid 24 through 32 Processing helix chain 'X' and resid 34 through 81 Processing helix chain 'r' and resid 92 through 99 Processing helix chain 'r' and resid 102 through 108 Processing helix chain 'r' and resid 119 through 132 Processing helix chain 'J' and resid 442 through 466 Processing helix chain 'J' and resid 481 through 491 removed outlier: 7.481A pdb=" N THR J 487 " --> pdb=" O ARG J 483 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU J 488 " --> pdb=" O VAL J 484 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN J 491 " --> pdb=" O THR J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 493 through 517 Processing helix chain 'J' and resid 522 through 532 Processing helix chain 'J' and resid 554 through 566 Processing helix chain 'J' and resid 588 through 600 Processing helix chain 'J' and resid 654 through 663 Processing helix chain 'J' and resid 667 through 682 Processing helix chain 'L' and resid 54 through 79 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 89 through 120 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) removed outlier: 4.410A pdb=" N LYS L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 removed outlier: 4.013A pdb=" N GLU L 126 " --> pdb=" O PRO L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 142 Processing helix chain 'L' and resid 154 through 158 Processing helix chain 'L' and resid 161 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 181 through 215 removed outlier: 5.320A pdb=" N SER L 213 " --> pdb=" O GLU L 209 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE L 214 " --> pdb=" O SER L 210 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE L 215 " --> pdb=" O ARG L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 235 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 238 through 242 Processing helix chain 'L' and resid 246 through 250 Processing helix chain 'L' and resid 278 through 281 No H-bonds generated for 'chain 'L' and resid 278 through 281' Processing helix chain 'L' and resid 285 through 308 removed outlier: 3.578A pdb=" N ARG L 288 " --> pdb=" O PRO L 285 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ARG L 289 " --> pdb=" O ASP L 286 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS L 290 " --> pdb=" O LEU L 287 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA L 291 " --> pdb=" O ARG L 288 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER L 307 " --> pdb=" O ARG L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 331 Processing helix chain 'L' and resid 357 through 366 Processing helix chain 'L' and resid 370 through 375 Processing helix chain 'L' and resid 414 through 416 No H-bonds generated for 'chain 'L' and resid 414 through 416' Processing helix chain 'L' and resid 422 through 431 Processing helix chain 'F' and resid 89 through 98 removed outlier: 3.519A pdb=" N GLN F 98 " --> pdb=" O LYS F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 115 Processing helix chain 'F' and resid 126 through 139 Processing helix chain 'F' and resid 173 through 201 Proline residue: F 187 - end of helix Processing helix chain 'F' and resid 204 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 117 through 134 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 138 through 151 removed outlier: 3.517A pdb=" N PHE N 142 " --> pdb=" O ILE N 138 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASP N 144 " --> pdb=" O GLN N 140 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LEU N 145 " --> pdb=" O GLN N 141 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU N 149 " --> pdb=" O LEU N 145 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA N 150 " --> pdb=" O LYS N 146 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLU N 151 " --> pdb=" O ARG N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 154 through 158 Processing helix chain 'N' and resid 169 through 172 No H-bonds generated for 'chain 'N' and resid 169 through 172' Processing helix chain 'N' and resid 184 through 193 Processing helix chain 'N' and resid 291 through 304 Processing helix chain 'N' and resid 309 through 322 Processing helix chain 'N' and resid 325 through 338 Processing helix chain 'N' and resid 343 through 352 Processing helix chain 'N' and resid 355 through 368 Processing helix chain 'N' and resid 373 through 382 Processing helix chain 'N' and resid 386 through 399 removed outlier: 4.150A pdb=" N HIS N 399 " --> pdb=" O LYS N 395 " (cutoff:3.500A) Processing helix chain 'N' and resid 404 through 413 removed outlier: 3.896A pdb=" N LEU N 413 " --> pdb=" O ALA N 409 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 429 Processing helix chain 'N' and resid 434 through 443 Processing helix chain 'N' and resid 450 through 459 Processing helix chain 'N' and resid 464 through 476 Processing helix chain 'N' and resid 480 through 497 Processing helix chain 'N' and resid 503 through 515 Processing helix chain 'N' and resid 519 through 531 Processing helix chain 'N' and resid 541 through 552 Processing helix chain 'N' and resid 559 through 568 Processing helix chain 'N' and resid 574 through 586 Processing helix chain 'N' and resid 590 through 603 Processing helix chain 'N' and resid 608 through 620 removed outlier: 3.697A pdb=" N LEU N 612 " --> pdb=" O GLU N 608 " (cutoff:3.500A) Processing helix chain 'N' and resid 624 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 644 through 655 removed outlier: 3.613A pdb=" N GLU N 654 " --> pdb=" O LYS N 650 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN N 655 " --> pdb=" O LEU N 651 " (cutoff:3.500A) Processing helix chain 'N' and resid 660 through 670 Processing helix chain 'N' and resid 675 through 687 Processing helix chain 'N' and resid 691 through 704 removed outlier: 3.633A pdb=" N LEU N 697 " --> pdb=" O ALA N 693 " (cutoff:3.500A) Processing helix chain 'N' and resid 709 through 721 Processing helix chain 'N' and resid 726 through 738 Processing helix chain 'N' and resid 743 through 756 Processing helix chain 'N' and resid 759 through 772 Processing helix chain 'N' and resid 777 through 789 removed outlier: 3.552A pdb=" N GLU N 787 " --> pdb=" O SER N 783 " (cutoff:3.500A) Processing helix chain 'N' and resid 793 through 805 Processing helix chain 'N' and resid 811 through 820 removed outlier: 3.802A pdb=" N PHE N 819 " --> pdb=" O SER N 815 " (cutoff:3.500A) Processing helix chain 'N' and resid 827 through 837 removed outlier: 3.628A pdb=" N VAL N 831 " --> pdb=" O ARG N 827 " (cutoff:3.500A) Processing helix chain 'N' and resid 841 through 853 Processing helix chain 'N' and resid 857 through 869 Processing helix chain 'N' and resid 877 through 887 Processing helix chain 'N' and resid 892 through 903 removed outlier: 3.516A pdb=" N ARG N 898 " --> pdb=" O GLN N 894 " (cutoff:3.500A) Processing helix chain 'N' and resid 910 through 919 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 925 through 927 No H-bonds generated for 'chain 'N' and resid 925 through 927' Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 93 through 105 Proline residue: A 96 - end of helix removed outlier: 3.637A pdb=" N LEU A 103 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU A 104 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 157 Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 201 through 204 No H-bonds generated for 'chain 'A' and resid 201 through 204' Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 317 through 320 No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 398 through 405 Processing helix chain 'A' and resid 409 through 412 No H-bonds generated for 'chain 'A' and resid 409 through 412' Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 428 through 431 No H-bonds generated for 'chain 'A' and resid 428 through 431' Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 489 through 510 removed outlier: 3.546A pdb=" N ARG A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 542 through 565 Processing helix chain 'A' and resid 571 through 588 removed outlier: 6.279A pdb=" N GLY A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 594 No H-bonds generated for 'chain 'A' and resid 591 through 594' Processing helix chain 'A' and resid 596 through 616 Processing helix chain 'A' and resid 631 through 656 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 695 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) Processing helix chain 'A' and resid 699 through 721 removed outlier: 4.782A pdb=" N GLN A 703 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 704 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A 705 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ALA A 706 " --> pdb=" O GLN A 703 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ARG A 707 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 709 " --> pdb=" O ALA A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 763 Processing helix chain 'A' and resid 769 through 797 Processing helix chain 'A' and resid 803 through 819 Processing helix chain 'A' and resid 833 through 850 removed outlier: 4.493A pdb=" N THR A 836 " --> pdb=" O LYS A 833 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 838 " --> pdb=" O ASP A 835 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 849 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 872 Processing helix chain 'A' and resid 874 through 887 Processing helix chain 'A' and resid 913 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 948 through 961 Processing helix chain 'A' and resid 990 through 999 removed outlier: 4.008A pdb=" N LEU A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1012 Processing helix chain 'A' and resid 1037 through 1062 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 1077 through 1080 No H-bonds generated for 'chain 'A' and resid 1077 through 1080' Processing helix chain 'A' and resid 1103 through 1116 removed outlier: 3.639A pdb=" N GLU A1116 " --> pdb=" O ARG A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1159 Processing helix chain 'A' and resid 1234 through 1249 Processing helix chain 'A' and resid 1256 through 1273 removed outlier: 3.612A pdb=" N TYR A1273 " --> pdb=" O GLY A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1280 No H-bonds generated for 'chain 'A' and resid 1277 through 1280' Processing helix chain 'A' and resid 1282 through 1303 Processing helix chain 'A' and resid 1314 through 1317 No H-bonds generated for 'chain 'A' and resid 1314 through 1317' Processing helix chain 'A' and resid 1320 through 1322 No H-bonds generated for 'chain 'A' and resid 1320 through 1322' Processing helix chain 'A' and resid 1337 through 1339 No H-bonds generated for 'chain 'A' and resid 1337 through 1339' Processing helix chain 'A' and resid 1368 through 1371 Processing helix chain 'A' and resid 1375 through 1398 Processing helix chain 'A' and resid 1419 through 1423 Processing helix chain 'A' and resid 1427 through 1432 removed outlier: 4.734A pdb=" N TYR A1432 " --> pdb=" O HIS A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1445 removed outlier: 4.620A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1477 Processing helix chain 'A' and resid 1480 through 1487 removed outlier: 4.128A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1493 No H-bonds generated for 'chain 'A' and resid 1491 through 1493' Processing helix chain 'A' and resid 1508 through 1515 removed outlier: 4.157A pdb=" N TRP A1515 " --> pdb=" O GLU A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1527 Processing helix chain 'A' and resid 1529 through 1537 Processing helix chain 'A' and resid 1539 through 1542 No H-bonds generated for 'chain 'A' and resid 1539 through 1542' Processing helix chain 'A' and resid 1567 through 1576 removed outlier: 4.031A pdb=" N SER A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1599 Processing helix chain 'A' and resid 1676 through 1687 Processing helix chain 'A' and resid 1722 through 1735 removed outlier: 4.139A pdb=" N GLN A1728 " --> pdb=" O PRO A1724 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1751 Processing helix chain 'A' and resid 1769 through 1771 No H-bonds generated for 'chain 'A' and resid 1769 through 1771' Processing helix chain 'A' and resid 1824 through 1827 Processing helix chain 'A' and resid 1833 through 1851 Processing helix chain 'A' and resid 1854 through 1856 No H-bonds generated for 'chain 'A' and resid 1854 through 1856' Processing helix chain 'A' and resid 1866 through 1875 removed outlier: 4.114A pdb=" N ASP A1870 " --> pdb=" O GLY A1867 " (cutoff:3.500A) Proline residue: A1871 - end of helix removed outlier: 3.529A pdb=" N VAL A1874 " --> pdb=" O PRO A1871 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1898 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 1900 through 1908 removed outlier: 3.793A pdb=" N LEU A1905 " --> pdb=" O LYS A1901 " (cutoff:3.500A) Processing helix chain 'A' and resid 1929 through 1945 Processing helix chain 'A' and resid 1947 through 1954 Processing helix chain 'A' and resid 1973 through 1995 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 2004 through 2011 Processing helix chain 'A' and resid 2021 through 2030 Processing helix chain 'A' and resid 2073 through 2080 removed outlier: 3.771A pdb=" N ILE A2078 " --> pdb=" O ARG A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2083 through 2088 removed outlier: 3.655A pdb=" N ASN A2088 " --> pdb=" O LEU A2085 " (cutoff:3.500A) Processing helix chain 'A' and resid 2108 through 2117 Processing helix chain 'A' and resid 2190 through 2201 Processing helix chain 'A' and resid 2232 through 2240 Processing helix chain 'A' and resid 2253 through 2255 No H-bonds generated for 'chain 'A' and resid 2253 through 2255' Processing helix chain 'A' and resid 2311 through 2316 Processing helix chain 'S' and resid 158 through 184 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 201 through 218 Processing helix chain 'S' and resid 263 through 265 No H-bonds generated for 'chain 'S' and resid 263 through 265' Processing helix chain 'S' and resid 292 through 308 Processing helix chain 'S' and resid 329 through 335 removed outlier: 4.353A pdb=" N ILE S 333 " --> pdb=" O PRO S 330 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER S 335 " --> pdb=" O SER S 332 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '7' and resid 410 through 412 Processing sheet with id= B, first strand: chain 'C' and resid 316 through 318 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) removed outlier: 6.570A pdb=" N LEU C 199 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL C 132 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASN C 201 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU C 134 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET C 203 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLY C 136 " --> pdb=" O MET C 203 " (cutoff:3.500A) Processing sheet with id= C, 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= D, first strand: chain 'C' and resid 523 through 526 removed outlier: 6.923A pdb=" N PHE C 493 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET C 481 " --> pdb=" O HIS C 491 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N HIS C 491 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 494 " --> pdb=" O VAL C 550 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 530 through 534 removed outlier: 3.895A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 653 through 655 removed outlier: 4.186A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 663 through 666 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= H, first strand: chain 'C' and resid 674 through 677 removed outlier: 7.033A pdb=" N ILE C 688 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE C 791 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLU C 690 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N PHE C 789 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 734 " --> pdb=" O LEU C 745 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP C 747 " --> pdb=" O ILE C 732 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE C 732 " --> pdb=" O ASP C 747 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 831 through 838 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= J, first strand: chain 'D' and resid 56 through 62 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= K, first strand: chain 'D' and resid 91 through 93 Processing sheet with id= L, first strand: chain 'I' and resid 129 through 133 Processing sheet with id= M, first strand: chain 'M' and resid 35 through 37 removed outlier: 3.874A pdb=" N PHE M 53 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N MET M 56 " --> pdb=" O PRO M 79 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL M 81 " --> pdb=" O MET M 56 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'U' and resid 134 through 136 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) removed outlier: 3.628A pdb=" N TYR U 179 " --> pdb=" O CYS U 174 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'U' and resid 381 through 388 removed outlier: 5.658A pdb=" N ARG U 354 " --> pdb=" O LEU U 443 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU U 443 " --> pdb=" O ARG U 354 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE U 356 " --> pdb=" O PHE U 441 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE U 441 " --> pdb=" O PHE U 356 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS U 358 " --> pdb=" O LYS U 439 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS U 439 " --> pdb=" O LYS U 358 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS U 428 " --> pdb=" O LYS U 439 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'U' and resid 391 through 393 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= Q, first strand: chain 'U' and resid 412 through 414 removed outlier: 6.348A pdb=" N ILE U 470 " --> pdb=" O VAL U 413 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'U' and resid 457 through 459 Processing sheet with id= S, first strand: chain 'X' and resid 10 through 13 Processing sheet with id= T, first strand: chain 'r' and resid 80 through 82 Processing sheet with id= U, first strand: chain 'J' and resid 570 through 575 removed outlier: 6.329A pdb=" N ARG J 547 " --> pdb=" O LEU J 632 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU J 632 " --> pdb=" O ARG J 547 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 234 through 239 removed outlier: 6.387A pdb=" N ALA F 249 " --> pdb=" O SER F 235 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N CYS F 237 " --> pdb=" O ALA F 247 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA F 247 " --> pdb=" O CYS F 237 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N PHE F 239 " --> pdb=" O MET F 245 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET F 245 " --> pdb=" O PHE F 239 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS F 267 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER F 259 " --> pdb=" O LEU F 265 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU F 265 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 317 through 319 removed outlier: 3.697A pdb=" N ALA F 317 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA F 278 " --> pdb=" O CYS F 299 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 326 through 331 removed outlier: 7.143A pdb=" N THR F 341 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL F 329 " --> pdb=" O GLY F 339 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY F 339 " --> pdb=" O VAL F 329 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TRP F 331 " --> pdb=" O PHE F 337 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE F 337 " --> pdb=" O TRP F 331 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER F 346 " --> pdb=" O CYS F 342 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU F 359 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ASP F 351 " --> pdb=" O GLU F 357 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLU F 357 " --> pdb=" O ASP F 351 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 368 through 373 removed outlier: 6.597A pdb=" N GLY F 383 " --> pdb=" O TYR F 369 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE F 371 " --> pdb=" O GLY F 381 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY F 381 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE F 373 " --> pdb=" O LEU F 379 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU F 379 " --> pdb=" O PHE F 373 " (cutoff:3.500A) 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= Z, 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= AA, first strand: chain 'F' and resid 452 through 457 removed outlier: 6.318A pdb=" N GLY F 468 " --> pdb=" O THR F 453 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL F 455 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU F 466 " --> pdb=" O VAL F 455 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE F 457 " --> pdb=" O PHE F 464 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE F 464 " --> pdb=" O PHE F 457 " (cutoff:3.500A) 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= AB, first strand: chain 'F' and resid 497 through 500 removed outlier: 3.808A pdb=" N GLY F 497 " --> pdb=" O CYS F 510 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS F 225 " --> pdb=" O LEU F 518 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET F 520 " --> pdb=" O ASN F 223 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ASN F 223 " --> pdb=" O MET F 520 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 482 through 488 Processing sheet with id= AD, first strand: chain 'A' and resid 227 through 229 Processing sheet with id= AE, first strand: chain 'A' and resid 516 through 518 Processing sheet with id= AF, first strand: chain 'A' and resid 895 through 899 Processing sheet with id= AG, first strand: chain 'A' and resid 1174 through 1178 removed outlier: 3.609A pdb=" N VAL A 975 " --> pdb=" O PHE A1099 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 1016 through 1019 Processing sheet with id= AI, first strand: chain 'A' and resid 1184 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= AJ, first strand: chain 'A' and resid 1341 through 1345 Processing sheet with id= AK, first strand: chain 'A' and resid 1711 through 1716 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) removed outlier: 3.539A pdb=" N THR A1608 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'A' and resid 1637 through 1639 Processing sheet with id= AM, first strand: chain 'A' and resid 1913 through 1918 removed outlier: 3.730A pdb=" N GLN A1913 " --> pdb=" O ILE A1821 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN A1860 " --> pdb=" O TRP A1778 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A1780 " --> pdb=" O GLN A1860 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A1862 " --> pdb=" O VAL A1780 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A1883 " --> pdb=" O ILE A1861 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL A1863 " --> pdb=" O VAL A1883 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS A1885 " --> pdb=" O VAL A1863 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'A' and resid 1787 through 1792 removed outlier: 4.416A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'A' and resid 2042 through 2047 Processing sheet with id= AP, first strand: chain 'A' and resid 2104 through 2106 Processing sheet with id= AQ, first strand: chain 'A' and resid 2125 through 2127 removed outlier: 3.810A pdb=" N ILE A2214 " --> pdb=" O TRP A2177 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA A2227 " --> pdb=" O VAL A2259 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'A' and resid 2272 through 2274 2060 hydrogen bonds defined for protein. 5610 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: 27.65 Time building geometry restraints manager: 18.53 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: 98.63 - 105.71: 2285 105.71 - 112.79: 30805 112.79 - 119.87: 18275 119.87 - 126.95: 24686 126.95 - 134.03: 1258 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: 4776 2.74 - 3.28: 54621 3.28 - 3.82: 97693 3.82 - 4.36: 116902 4.36 - 4.90: 190336 Nonbonded interactions: 464328 Sorted by model distance: nonbonded pdb=" OD2 ASP A1146 " pdb=" ND2 ASN A1182 " model vdw 2.202 2.520 nonbonded pdb=" OG1 THR A1102 " pdb=" OD1 ASP A1104 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR A1091 " pdb=" OD2 ASP A1441 " model vdw 2.206 2.440 nonbonded pdb=" OG SER F 259 " pdb=" O ASP F 262 " model vdw 2.211 2.440 nonbonded pdb=" OE1 GLN I 18 " pdb=" OH TYR I 30 " model vdw 2.222 2.440 ... (remaining 464323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 6.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 24.220 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 128.120 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.190 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.770 ------------------------------------------------------------------------------- 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= 0.162 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 : 4.462 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: 0.4866 time to fit residues: 193.3947 Evaluate side-chains 195 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 4.469 ------------------------------------------------------------------------------- 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: 0.9980 chunk 485 optimal weight: 0.9990 chunk 269 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 chunk 259 optimal weight: 0.8980 chunk 502 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 chunk 373 optimal weight: 0.9980 chunk 582 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 GLN M 115 GLN ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN r 107 ASN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 515 ASN ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN A1014 ASN ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2032 GLN A2255 HIS ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 211 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 56235 Z= 0.165 Angle : 0.498 14.940 77309 Z= 0.250 Chirality : 0.042 1.090 8789 Planarity : 0.004 0.055 9073 Dihedral : 15.742 179.775 10467 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.19 % Allowed : 3.73 % Favored : 96.08 % 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: 1.28 (0.11), residues: 6199 helix: 1.79 (0.10), residues: 2879 sheet: 0.07 (0.19), residues: 755 loop : 0.12 (0.13), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 750 HIS 0.005 0.001 HIS A1674 PHE 0.022 0.001 PHE J 594 TYR 0.014 0.001 TYR A1044 ARG 0.005 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 207 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 4.575 Fit side-chains revert: symmetry clash REVERT: r 57 ASP cc_start: 0.7332 (p0) cc_final: 0.7018 (p0) REVERT: J 536 ASP cc_start: 0.6707 (p0) cc_final: 0.6469 (p0) REVERT: S 356 THR cc_start: 0.8060 (p) cc_final: 0.7834 (p) outliers start: 10 outliers final: 7 residues processed: 203 average time/residue: 0.4784 time to fit residues: 176.3963 Evaluate side-chains 199 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 192 time to evaluate : 4.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain I residue 115 ASP 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 199 ASP 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: 0.0670 chunk 484 optimal weight: 2.9990 chunk 396 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 chunk 583 optimal weight: 0.7980 chunk 629 optimal weight: 0.9980 chunk 519 optimal weight: 3.9990 chunk 578 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 467 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 GLN M 115 GLN U 200 GLN ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 376 ASN ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 308 HIS A1014 ASN A1227 GLN ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2181 GLN A2309 HIS S 211 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 56235 Z= 0.134 Angle : 0.454 8.487 77309 Z= 0.230 Chirality : 0.038 0.488 8789 Planarity : 0.003 0.053 9073 Dihedral : 15.690 179.189 10467 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.44 % Allowed : 5.30 % Favored : 94.26 % 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: 1.31 (0.11), residues: 6199 helix: 1.81 (0.10), residues: 2878 sheet: 0.09 (0.19), residues: 752 loop : 0.14 (0.13), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 750 HIS 0.004 0.001 HIS A1674 PHE 0.010 0.001 PHE A1719 TYR 0.012 0.001 TYR A1044 ARG 0.004 0.000 ARG A1195 *********************** 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 222 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 199 time to evaluate : 4.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 687 MET cc_start: 0.8282 (ttm) cc_final: 0.7910 (ttm) REVERT: U 389 MET cc_start: 0.7728 (tpp) cc_final: 0.7204 (tpp) REVERT: J 536 ASP cc_start: 0.6760 (p0) cc_final: 0.6491 (p0) REVERT: F 401 MET cc_start: 0.8355 (ttt) cc_final: 0.7878 (ttt) REVERT: N 112 MET cc_start: 0.9092 (mmp) cc_final: 0.8817 (mmp) REVERT: A 76 MET cc_start: 0.2672 (mmm) cc_final: 0.2407 (mmp) REVERT: A 1227 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8098 (mt0) REVERT: S 356 THR cc_start: 0.8040 (p) cc_final: 0.7811 (p) outliers start: 23 outliers final: 13 residues processed: 215 average time/residue: 0.4921 time to fit residues: 190.2496 Evaluate side-chains 206 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 192 time to evaluate : 4.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain N residue 484 GLU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 641 random chunks: chunk 576 optimal weight: 2.9990 chunk 438 optimal weight: 4.9990 chunk 302 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 278 optimal weight: 1.9990 chunk 391 optimal weight: 5.9990 chunk 585 optimal weight: 3.9990 chunk 619 optimal weight: 7.9990 chunk 305 optimal weight: 10.0000 chunk 554 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 GLN M 115 GLN U 151 HIS U 200 GLN U 407 GLN ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN ** 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** ** F 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 307 HIS A 792 HIS ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 211 GLN S 328 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 56235 Z= 0.396 Angle : 0.565 8.953 77309 Z= 0.287 Chirality : 0.043 0.534 8789 Planarity : 0.004 0.069 9073 Dihedral : 15.698 178.875 10467 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.80 % Allowed : 7.40 % Favored : 91.79 % 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: 1.05 (0.11), residues: 6199 helix: 1.58 (0.10), residues: 2891 sheet: -0.01 (0.19), residues: 740 loop : 0.02 (0.13), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 293 HIS 0.008 0.001 HIS A1674 PHE 0.018 0.002 PHE C 339 TYR 0.021 0.002 TYR A1091 ARG 0.009 0.001 ARG A1667 *********************** 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 236 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 4.632 Fit side-chains revert: symmetry clash REVERT: C 687 MET cc_start: 0.8381 (ttm) cc_final: 0.8038 (ttm) REVERT: U 281 MET cc_start: 0.7707 (tpt) cc_final: 0.7354 (tpt) REVERT: J 536 ASP cc_start: 0.6871 (p0) cc_final: 0.6560 (p0) REVERT: F 401 MET cc_start: 0.8338 (ttt) cc_final: 0.7882 (ttt) REVERT: N 679 MET cc_start: 0.7483 (ppp) cc_final: 0.6932 (ppp) REVERT: N 800 MET cc_start: 0.8783 (tpp) cc_final: 0.8520 (tpp) REVERT: A 1327 MET cc_start: 0.8633 (tpp) cc_final: 0.8412 (ttt) REVERT: A 1889 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8630 (pt) REVERT: A 1937 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9167 (mm) REVERT: S 356 THR cc_start: 0.8088 (p) cc_final: 0.7851 (p) outliers start: 42 outliers final: 20 residues processed: 227 average time/residue: 0.5431 time to fit residues: 224.4452 Evaluate side-chains 214 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 4.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain 7 residue 482 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain r residue 77 MET 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 951 LEU Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1558 THR 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 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: 7.9990 chunk 9 optimal weight: 8.9990 chunk 461 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 528 optimal weight: 0.8980 chunk 428 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 316 optimal weight: 2.9990 chunk 556 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 16 ASN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 GLN M 115 GLN ** U 530 GLN ** 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** ** F 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 GLN ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 56235 Z= 0.208 Angle : 0.484 9.194 77309 Z= 0.246 Chirality : 0.039 0.416 8789 Planarity : 0.004 0.053 9073 Dihedral : 15.698 179.975 10467 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.80 % Allowed : 8.44 % Favored : 90.76 % 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: 1.12 (0.11), residues: 6199 helix: 1.64 (0.10), residues: 2893 sheet: -0.07 (0.19), residues: 730 loop : 0.07 (0.13), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 750 HIS 0.005 0.001 HIS A1674 PHE 0.012 0.001 PHE A1274 TYR 0.011 0.001 TYR A 614 ARG 0.004 0.000 ARG A1195 *********************** 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 235 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 193 time to evaluate : 4.500 Fit side-chains revert: symmetry clash REVERT: U 281 MET cc_start: 0.7698 (tpt) cc_final: 0.7469 (tpt) REVERT: J 536 ASP cc_start: 0.6882 (p0) cc_final: 0.6563 (p0) REVERT: L 184 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8197 (mm) REVERT: F 401 MET cc_start: 0.8286 (ttt) cc_final: 0.7856 (ttt) REVERT: F 498 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8843 (pp) REVERT: N 338 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7396 (ttp) REVERT: N 482 MET cc_start: 0.7330 (mmp) cc_final: 0.7047 (mmp) REVERT: N 679 MET cc_start: 0.7473 (ppp) cc_final: 0.6920 (ppp) REVERT: N 800 MET cc_start: 0.8884 (tpp) cc_final: 0.8442 (tpp) REVERT: A 1237 MET cc_start: 0.8442 (mtm) cc_final: 0.8191 (mtm) REVERT: A 1340 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9122 (mt) REVERT: S 356 THR cc_start: 0.8050 (p) cc_final: 0.7817 (p) outliers start: 42 outliers final: 24 residues processed: 222 average time/residue: 0.4866 time to fit residues: 193.4939 Evaluate side-chains 220 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 4.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain 7 residue 482 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 338 MET Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 599 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 1340 LEU Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1558 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 641 random chunks: chunk 208 optimal weight: 3.9990 chunk 557 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 363 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 620 optimal weight: 2.9990 chunk 514 optimal weight: 0.5980 chunk 287 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 325 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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** M 28 GLN M 115 GLN ** U 530 GLN ** 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** ** F 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 56235 Z= 0.279 Angle : 0.513 10.084 77309 Z= 0.260 Chirality : 0.040 0.403 8789 Planarity : 0.004 0.056 9073 Dihedral : 15.680 179.238 10467 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.96 % Allowed : 9.33 % Favored : 89.71 % 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: 1.08 (0.11), residues: 6199 helix: 1.60 (0.10), residues: 2892 sheet: -0.07 (0.19), residues: 725 loop : 0.05 (0.13), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 750 HIS 0.006 0.001 HIS A1674 PHE 0.014 0.001 PHE C 493 TYR 0.013 0.001 TYR A1091 ARG 0.006 0.000 ARG A1195 *********************** 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 244 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 194 time to evaluate : 4.517 Fit side-chains revert: symmetry clash REVERT: 7 449 LYS cc_start: 0.7096 (pttp) cc_final: 0.6153 (pttm) REVERT: U 283 LYS cc_start: 0.8293 (mtmt) cc_final: 0.8068 (mmtp) REVERT: J 536 ASP cc_start: 0.6845 (p0) cc_final: 0.6636 (p0) REVERT: L 184 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8246 (mm) REVERT: F 401 MET cc_start: 0.8287 (ttt) cc_final: 0.7851 (ttt) REVERT: F 498 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8806 (pp) REVERT: N 679 MET cc_start: 0.7485 (ppp) cc_final: 0.6919 (ppp) REVERT: N 800 MET cc_start: 0.8927 (tpp) cc_final: 0.8398 (tpp) REVERT: A 1340 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9153 (mt) REVERT: S 356 THR cc_start: 0.8061 (p) cc_final: 0.7821 (p) outliers start: 50 outliers final: 32 residues processed: 231 average time/residue: 0.4787 time to fit residues: 199.4280 Evaluate side-chains 226 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 191 time to evaluate : 4.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain 7 residue 482 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain r residue 77 MET 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 F residue 429 ASN Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 599 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 1340 LEU Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1558 THR Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1874 VAL Chi-restraints excluded: chain A residue 1889 LEU Chi-restraints excluded: chain A residue 2016 ILE Chi-restraints excluded: chain A residue 2153 THR 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 ************** Weight determination summary: number of chunks: 641 random chunks: chunk 597 optimal weight: 0.0470 chunk 69 optimal weight: 0.5980 chunk 353 optimal weight: 0.5980 chunk 452 optimal weight: 0.8980 chunk 350 optimal weight: 2.9990 chunk 522 optimal weight: 0.6980 chunk 346 optimal weight: 3.9990 chunk 617 optimal weight: 8.9990 chunk 386 optimal weight: 2.9990 chunk 376 optimal weight: 5.9990 chunk 285 optimal weight: 10.0000 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 GLN M 115 GLN U 200 GLN ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 ASN ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2255 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 56235 Z= 0.134 Angle : 0.457 10.783 77309 Z= 0.231 Chirality : 0.037 0.309 8789 Planarity : 0.003 0.053 9073 Dihedral : 15.651 179.882 10467 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.65 % Allowed : 9.83 % Favored : 89.52 % 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: 1.26 (0.11), residues: 6199 helix: 1.78 (0.10), residues: 2888 sheet: -0.03 (0.19), residues: 747 loop : 0.13 (0.13), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 750 HIS 0.004 0.001 HIS A1674 PHE 0.012 0.001 PHE A1274 TYR 0.013 0.001 TYR A 614 ARG 0.004 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 7 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 228 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 4.505 Fit side-chains revert: symmetry clash REVERT: U 283 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7989 (mmtp) REVERT: J 536 ASP cc_start: 0.6833 (p0) cc_final: 0.6627 (p0) REVERT: L 392 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8389 (mt) REVERT: F 401 MET cc_start: 0.8246 (ttt) cc_final: 0.7819 (ttt) REVERT: F 498 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8812 (pp) REVERT: N 482 MET cc_start: 0.7113 (mmp) cc_final: 0.6865 (mmp) REVERT: N 679 MET cc_start: 0.7473 (ppp) cc_final: 0.6904 (ppp) REVERT: N 800 MET cc_start: 0.8935 (tpp) cc_final: 0.8703 (tpp) REVERT: A 1327 MET cc_start: 0.8007 (ttt) cc_final: 0.7787 (ttt) REVERT: A 1340 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9125 (mt) REVERT: S 356 THR cc_start: 0.8016 (p) cc_final: 0.7780 (p) outliers start: 34 outliers final: 23 residues processed: 220 average time/residue: 0.4912 time to fit residues: 194.6157 Evaluate side-chains 218 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 4.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain J residue 485 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 392 LEU Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 599 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 1340 LEU Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1438 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 641 random chunks: chunk 382 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 368 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 392 optimal weight: 0.9990 chunk 420 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 485 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 GLN M 115 GLN U 200 GLN U 372 GLN ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2255 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 56235 Z= 0.243 Angle : 0.496 11.480 77309 Z= 0.250 Chirality : 0.039 0.320 8789 Planarity : 0.004 0.053 9073 Dihedral : 15.620 179.640 10467 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.94 % Allowed : 9.97 % Favored : 89.10 % 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: 1.23 (0.11), residues: 6199 helix: 1.75 (0.10), residues: 2887 sheet: -0.05 (0.19), residues: 757 loop : 0.11 (0.13), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 750 HIS 0.006 0.001 HIS A1674 PHE 0.017 0.001 PHE J 594 TYR 0.012 0.001 TYR D 3 ARG 0.005 0.000 ARG A1195 *********************** REFINEMENT MACRO_CYCLE 8 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 242 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 193 time to evaluate : 4.472 Fit side-chains revert: symmetry clash REVERT: C 133 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8122 (m) REVERT: U 389 MET cc_start: 0.7564 (tpp) cc_final: 0.6916 (tpp) REVERT: J 536 ASP cc_start: 0.6949 (p0) cc_final: 0.6698 (p0) REVERT: L 184 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8263 (mm) REVERT: L 392 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8593 (mt) REVERT: F 401 MET cc_start: 0.8269 (ttt) cc_final: 0.7841 (ttt) REVERT: F 498 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8801 (pp) REVERT: N 679 MET cc_start: 0.7485 (ppp) cc_final: 0.6907 (ppp) REVERT: N 800 MET cc_start: 0.8952 (tpp) cc_final: 0.8694 (tpp) REVERT: A 1327 MET cc_start: 0.8464 (ttt) cc_final: 0.8193 (ttt) REVERT: A 1340 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9168 (mt) REVERT: S 356 THR cc_start: 0.8042 (p) cc_final: 0.7800 (p) outliers start: 49 outliers final: 37 residues processed: 232 average time/residue: 0.5221 time to fit residues: 218.1346 Evaluate side-chains 233 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 191 time to evaluate : 4.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain 7 residue 482 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain J residue 485 LEU Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 392 LEU Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 843 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 599 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 1340 LEU Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1874 VAL Chi-restraints excluded: chain A residue 1889 LEU Chi-restraints excluded: chain A residue 1945 VAL Chi-restraints excluded: chain A residue 1962 THR Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2157 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 641 random chunks: chunk 562 optimal weight: 0.8980 chunk 591 optimal weight: 0.6980 chunk 540 optimal weight: 0.0030 chunk 575 optimal weight: 6.9990 chunk 346 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 452 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 520 optimal weight: 1.9990 chunk 544 optimal weight: 0.8980 chunk 573 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** U 200 GLN ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2255 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 56235 Z= 0.138 Angle : 0.459 11.675 77309 Z= 0.231 Chirality : 0.037 0.244 8789 Planarity : 0.003 0.053 9073 Dihedral : 15.606 179.516 10467 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.73 % Allowed : 10.31 % Favored : 88.96 % 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: 1.32 (0.11), residues: 6199 helix: 1.83 (0.10), residues: 2885 sheet: 0.02 (0.19), residues: 758 loop : 0.15 (0.13), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 750 HIS 0.004 0.001 HIS A1674 PHE 0.010 0.001 PHE A1274 TYR 0.012 0.001 TYR A 614 ARG 0.005 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 9 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 233 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 4.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8047 (m) REVERT: J 536 ASP cc_start: 0.6935 (p0) cc_final: 0.6693 (p0) REVERT: J 598 MET cc_start: 0.7224 (mpp) cc_final: 0.6930 (mtt) REVERT: L 184 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8255 (mm) REVERT: L 392 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8436 (mt) REVERT: F 401 MET cc_start: 0.8260 (ttt) cc_final: 0.7852 (ttt) REVERT: F 498 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8793 (pp) REVERT: N 679 MET cc_start: 0.7483 (ppp) cc_final: 0.6907 (ppp) REVERT: N 800 MET cc_start: 0.8955 (tpp) cc_final: 0.8698 (tpp) REVERT: A 1327 MET cc_start: 0.8068 (ttt) cc_final: 0.7801 (ttt) REVERT: A 1340 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9151 (mt) REVERT: S 356 THR cc_start: 0.8061 (p) cc_final: 0.7835 (p) outliers start: 38 outliers final: 32 residues processed: 223 average time/residue: 0.5048 time to fit residues: 202.7349 Evaluate side-chains 229 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 4.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain U residue 491 VAL Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain J residue 485 LEU Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 392 LEU Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 599 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 1340 LEU Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1962 THR Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2157 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 641 random chunks: chunk 378 optimal weight: 8.9990 chunk 608 optimal weight: 0.7980 chunk 371 optimal weight: 3.9990 chunk 288 optimal weight: 7.9990 chunk 423 optimal weight: 0.7980 chunk 638 optimal weight: 3.9990 chunk 587 optimal weight: 4.9990 chunk 508 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 392 optimal weight: 4.9990 chunk 311 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** U 200 GLN ** U 530 GLN ** 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 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2255 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 56235 Z= 0.262 Angle : 0.506 12.015 77309 Z= 0.254 Chirality : 0.039 0.285 8789 Planarity : 0.004 0.053 9073 Dihedral : 15.578 179.961 10467 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.84 % Allowed : 10.44 % Favored : 88.71 % 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: 1.23 (0.11), residues: 6199 helix: 1.75 (0.10), residues: 2892 sheet: -0.06 (0.19), residues: 738 loop : 0.11 (0.13), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 750 HIS 0.006 0.001 HIS D 32 PHE 0.012 0.001 PHE A 898 TYR 0.013 0.001 TYR D 3 ARG 0.009 0.000 ARG L 91 ********************** REFINEMENT MACRO_CYCLE 10 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 237 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 193 time to evaluate : 4.501 Fit side-chains revert: symmetry clash REVERT: C 133 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8135 (m) REVERT: U 389 MET cc_start: 0.7584 (tpp) cc_final: 0.6867 (tpp) REVERT: J 536 ASP cc_start: 0.6899 (p0) cc_final: 0.6661 (p0) REVERT: L 184 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8253 (mm) REVERT: L 392 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8644 (mt) REVERT: F 401 MET cc_start: 0.8258 (ttt) cc_final: 0.7824 (ttt) REVERT: F 498 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8801 (pp) REVERT: N 482 MET cc_start: 0.7115 (mmp) cc_final: 0.6879 (mmp) REVERT: N 679 MET cc_start: 0.7496 (ppp) cc_final: 0.6914 (ppp) REVERT: N 800 MET cc_start: 0.8973 (tpp) cc_final: 0.8686 (tpp) REVERT: A 1327 MET cc_start: 0.8478 (ttt) cc_final: 0.8234 (ttt) REVERT: A 1340 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9177 (mt) REVERT: S 356 THR cc_start: 0.8096 (p) cc_final: 0.7865 (p) outliers start: 44 outliers final: 36 residues processed: 226 average time/residue: 0.5088 time to fit residues: 208.2549 Evaluate side-chains 233 residues out of total 5545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 192 time to evaluate : 4.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain U residue 491 VAL Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain J residue 485 LEU Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 392 LEU Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 599 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 1340 LEU Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1874 VAL Chi-restraints excluded: chain A residue 1945 VAL Chi-restraints excluded: chain A residue 1962 THR Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2157 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 641 random chunks: chunk 403 optimal weight: 8.9990 chunk 541 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 468 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 141 optimal weight: 0.8980 chunk 509 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 523 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** U 200 GLN ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2255 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.079620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.060893 restraints weight = 186103.257| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.10 r_work: 0.3026 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 56235 Z= 0.147 Angle : 0.462 11.827 77309 Z= 0.232 Chirality : 0.037 0.244 8789 Planarity : 0.003 0.052 9073 Dihedral : 15.562 179.827 10467 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.80 % Allowed : 10.62 % Favored : 88.58 % 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: 1.30 (0.11), residues: 6199 helix: 1.80 (0.10), residues: 2893 sheet: 0.03 (0.19), residues: 756 loop : 0.15 (0.13), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 750 HIS 0.004 0.001 HIS A1674 PHE 0.010 0.001 PHE A1274 TYR 0.011 0.001 TYR A 614 ARG 0.008 0.000 ARG L 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8144.06 seconds wall clock time: 146 minutes 47.43 seconds (8807.43 seconds total)