Starting phenix.real_space_refine on Sat Aug 8 12:43:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yly_73097/08_2026/9yly_73097.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yly_73097/08_2026/9yly_73097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yly_73097/08_2026/9yly_73097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yly_73097/08_2026/9yly_73097.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yly_73097/08_2026/9yly_73097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yly_73097/08_2026/9yly_73097.map" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.057 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 330 5.49 5 S 120 5.16 5 C 16414 2.51 5 N 4975 2.21 5 O 5821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27668 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 875 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain breaks: 1 Chain: "F" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2326 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain: "N" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3238 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 2 Chain: "K" Number of atoms: 5825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5825 Classifications: {'peptide': 732} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 698} Chain breaks: 2 Chain: "T" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2446 Classifications: {'peptide': 304} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 278} Chain: "P" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "Q" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 432 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "I" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3401 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "J" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3364 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "K" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 34 Unusual residues: {' ZN': 8} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17063 SG CYS K5477 108.850 81.126 102.279 1.00 83.09 S ATOM 17457 SG CYS K5525 110.680 84.111 104.392 1.00 77.85 S ATOM 17473 SG CYS K5527 109.577 84.301 100.711 1.00 84.27 S ATOM 17510 SG CYS K5532 107.288 84.592 103.467 1.00 95.86 S ATOM 11918 SG CYS K1380 80.885 96.112 92.086 1.00179.56 S ATOM 11938 SG CYS K1383 80.854 92.437 92.364 1.00179.59 S ATOM 12122 SG CYS K1408 77.567 94.351 92.800 1.00185.40 S ATOM 12294 SG CYS K1430 60.538 112.288 97.454 1.00213.41 S ATOM 12316 SG CYS K1433 59.749 115.669 98.933 1.00214.85 S ATOM 12493 SG CYS K1456 57.133 113.678 96.775 1.00219.34 S ATOM 12402 SG CYS K1445 59.651 101.722 90.485 1.00230.29 S ATOM 12424 SG CYS K1448 62.293 103.606 88.662 1.00230.07 S ATOM 12606 SG CYS K1471 58.941 104.912 88.290 1.00235.86 S ATOM 12635 SG CYS K1474 59.761 101.301 86.810 1.00238.97 S ATOM 12654 SG CYS K1477 47.468 95.788 81.417 1.00322.50 S ATOM 12677 SG CYS K1480 45.133 96.969 78.555 1.00326.99 S ATOM 12816 SG CYS K1498 44.359 97.929 82.074 1.00338.79 S ATOM 12833 SG CYS K1501 44.042 94.289 81.042 1.00364.10 S ATOM 13533 SG CYS K5032 92.411 80.730 87.345 1.00153.88 S ATOM 13556 SG CYS K5035 92.639 78.231 84.805 1.00155.40 S ATOM 13993 SG CYS K5092 94.928 68.984 86.185 1.00146.75 S ATOM 14013 SG CYS K5095 96.514 71.003 82.671 1.00152.27 S ATOM 14184 SG CYS K5117 92.824 70.585 83.339 1.00153.92 S ATOM 14074 SG CYS K5104 85.786 60.131 93.983 1.00168.70 S ATOM 14118 SG CYS K5109 88.915 58.681 93.053 1.00165.33 S ATOM 14313 SG CYS K5133 86.607 58.696 90.470 1.00176.42 S Time building chain proxies: 4.14, per 1000 atoms: 0.15 Number of scatterers: 27668 At special positions: 0 Unit cell: (186.048, 149.872, 173.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 120 16.00 P 330 15.00 O 5821 8.00 N 4975 7.00 C 16414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 721.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K5601 " pdb="ZN ZN K5601 " - pdb=" SG CYS K5527 " pdb="ZN ZN K5601 " - pdb=" SG CYS K5532 " pdb="ZN ZN K5601 " - pdb=" SG CYS K5525 " pdb="ZN ZN K5601 " - pdb=" SG CYS K5477 " pdb=" ZN K5602 " pdb="ZN ZN K5602 " - pdb=" ND1 HIS K1405 " pdb="ZN ZN K5602 " - pdb=" SG CYS K1380 " pdb="ZN ZN K5602 " - pdb=" SG CYS K1383 " pdb="ZN ZN K5602 " - pdb=" SG CYS K1408 " pdb=" ZN K5603 " pdb="ZN ZN K5603 " - pdb=" ND1 HIS K1453 " pdb="ZN ZN K5603 " - pdb=" SG CYS K1430 " pdb="ZN ZN K5603 " - pdb=" SG CYS K1433 " pdb="ZN ZN K5603 " - pdb=" SG CYS K1456 " pdb=" ZN K5604 " pdb="ZN ZN K5604 " - pdb=" SG CYS K1448 " pdb="ZN ZN K5604 " - pdb=" SG CYS K1445 " pdb="ZN ZN K5604 " - pdb=" SG CYS K1471 " pdb="ZN ZN K5604 " - pdb=" SG CYS K1474 " pdb=" ZN K5605 " pdb="ZN ZN K5605 " - pdb=" SG CYS K1501 " pdb="ZN ZN K5605 " - pdb=" SG CYS K1498 " pdb="ZN ZN K5605 " - pdb=" SG CYS K1477 " pdb="ZN ZN K5605 " - pdb=" SG CYS K1480 " pdb=" ZN K5606 " pdb="ZN ZN K5606 " - pdb=" SG CYS K5032 " pdb="ZN ZN K5606 " - pdb=" ND1 HIS K5059 " pdb="ZN ZN K5606 " - pdb=" SG CYS K5035 " pdb=" ZN K5607 " pdb="ZN ZN K5607 " - pdb=" ND1 HIS K5114 " pdb="ZN ZN K5607 " - pdb=" SG CYS K5117 " pdb="ZN ZN K5607 " - pdb=" SG CYS K5095 " pdb="ZN ZN K5607 " - pdb=" SG CYS K5092 " pdb=" ZN K5608 " pdb="ZN ZN K5608 " - pdb=" ND1 HIS K5136 " pdb="ZN ZN K5608 " - pdb=" SG CYS K5104 " pdb="ZN ZN K5608 " - pdb=" SG CYS K5109 " pdb="ZN ZN K5608 " - pdb=" SG CYS K5133 " Number of angles added : 30 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4934 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 39 sheets defined 32.7% alpha, 14.8% beta 165 base pairs and 284 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.514A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.631A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.910A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.549A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.748A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.779A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 38 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.804A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.577A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.556A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.024A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.605A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.533A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.790A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.584A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.670A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.034A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.510A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.646A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 4.101A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 4.108A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.648A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.892A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 234 Processing helix chain 'N' and resid 348 through 353 removed outlier: 4.480A pdb=" N PHE N 352 " --> pdb=" O GLU N 349 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP N 353 " --> pdb=" O SER N 350 " (cutoff:3.500A) Processing helix chain 'N' and resid 468 through 472 Processing helix chain 'K' and resid 1414 through 1421 removed outlier: 3.560A pdb=" N LEU K1418 " --> pdb=" O THR K1414 " (cutoff:3.500A) Processing helix chain 'K' and resid 1424 through 1428 removed outlier: 3.690A pdb=" N ILE K1428 " --> pdb=" O VAL K1425 " (cutoff:3.500A) Processing helix chain 'K' and resid 1498 through 1506 removed outlier: 3.535A pdb=" N LEU K1504 " --> pdb=" O PRO K1500 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL K1505 " --> pdb=" O CYS K1501 " (cutoff:3.500A) Processing helix chain 'K' and resid 1533 through 1535 No H-bonds generated for 'chain 'K' and resid 1533 through 1535' Processing helix chain 'K' and resid 1539 through 1549 removed outlier: 3.996A pdb=" N VAL K1543 " --> pdb=" O THR K1539 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU K1544 " --> pdb=" O GLU K1540 " (cutoff:3.500A) Processing helix chain 'K' and resid 5007 through 5017 removed outlier: 3.591A pdb=" N MET K5013 " --> pdb=" O VAL K5009 " (cutoff:3.500A) Processing helix chain 'K' and resid 5060 through 5065 Processing helix chain 'K' and resid 5079 through 5089 removed outlier: 3.740A pdb=" N LEU K5089 " --> pdb=" O HIS K5085 " (cutoff:3.500A) Processing helix chain 'K' and resid 5114 through 5119 removed outlier: 3.892A pdb=" N ILE K5119 " --> pdb=" O PHE K5115 " (cutoff:3.500A) Processing helix chain 'K' and resid 5133 through 5137 Processing helix chain 'K' and resid 5160 through 5170 Processing helix chain 'K' and resid 5259 through 5277 removed outlier: 3.891A pdb=" N TRP K5264 " --> pdb=" O PRO K5260 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG K5266 " --> pdb=" O ALA K5262 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE K5267 " --> pdb=" O VAL K5263 " (cutoff:3.500A) Proline residue: K5270 - end of helix removed outlier: 3.730A pdb=" N ARG K5275 " --> pdb=" O VAL K5271 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU K5277 " --> pdb=" O ALA K5273 " (cutoff:3.500A) Processing helix chain 'K' and resid 5284 through 5288 Processing helix chain 'K' and resid 5289 through 5294 Processing helix chain 'K' and resid 5298 through 5308 Processing helix chain 'K' and resid 5383 through 5395 removed outlier: 3.584A pdb=" N ARG K5390 " --> pdb=" O SER K5386 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR K5393 " --> pdb=" O ARG K5389 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP K5395 " --> pdb=" O LEU K5391 " (cutoff:3.500A) Processing helix chain 'K' and resid 5432 through 5447 removed outlier: 4.090A pdb=" N GLU K5445 " --> pdb=" O LYS K5441 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN K5446 " --> pdb=" O ILE K5442 " (cutoff:3.500A) Processing helix chain 'K' and resid 5468 through 5472 removed outlier: 4.204A pdb=" N ARG K5471 " --> pdb=" O GLY K5468 " (cutoff:3.500A) Processing helix chain 'T' and resid 354 through 359 removed outlier: 3.985A pdb=" N LEU T 358 " --> pdb=" O ASP T 354 " (cutoff:3.500A) Processing helix chain 'T' and resid 369 through 371 No H-bonds generated for 'chain 'T' and resid 369 through 371' Processing helix chain 'T' and resid 496 through 501 Processing helix chain 'T' and resid 525 through 533 Processing helix chain 'T' and resid 596 through 619 removed outlier: 4.275A pdb=" N VAL T 602 " --> pdb=" O GLY T 598 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA T 608 " --> pdb=" O GLU T 604 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 59 removed outlier: 3.677A pdb=" N LEU P 57 " --> pdb=" O THR P 53 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN P 59 " --> pdb=" O ALA P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 76 removed outlier: 3.787A pdb=" N LEU P 65 " --> pdb=" O VAL P 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN P 67 " --> pdb=" O PRO P 63 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA P 70 " --> pdb=" O LEU P 66 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL P 71 " --> pdb=" O GLN P 67 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU P 75 " --> pdb=" O VAL P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 91 Processing helix chain 'P' and resid 91 through 97 removed outlier: 4.213A pdb=" N PHE P 95 " --> pdb=" O ASN P 91 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP P 97 " --> pdb=" O ALA P 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 59 removed outlier: 3.908A pdb=" N GLN Q 59 " --> pdb=" O ALA Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 76 removed outlier: 3.884A pdb=" N LEU Q 65 " --> pdb=" O VAL Q 61 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN Q 67 " --> pdb=" O PRO Q 63 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA Q 70 " --> pdb=" O LEU Q 66 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU Q 75 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 Processing helix chain 'Q' and resid 92 through 97 removed outlier: 4.105A pdb=" N ASP Q 97 " --> pdb=" O ALA Q 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.890A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.734A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.650A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.522A pdb=" N ARG K5454 " --> pdb=" O LYS E 4 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.014A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.582A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'R' and resid 36 through 40 removed outlier: 3.522A pdb=" N LYS R 331 " --> pdb=" O ALA R 36 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU R 329 " --> pdb=" O LYS R 38 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR R 40 " --> pdb=" O ILE R 327 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE R 327 " --> pdb=" O THR R 40 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA R 308 " --> pdb=" O ALA R 317 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER R 306 " --> pdb=" O ALA R 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 48 through 51 removed outlier: 3.799A pdb=" N LEU R 68 " --> pdb=" O SER R 64 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE R 83 " --> pdb=" O ILE R 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 94 through 95 removed outlier: 3.738A pdb=" N VAL R 103 " --> pdb=" O ALA R 94 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER R 106 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR R 110 " --> pdb=" O SER R 106 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU R 111 " --> pdb=" O THR R 124 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR R 124 " --> pdb=" O LEU R 111 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE R 113 " --> pdb=" O LEU R 122 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS R 120 " --> pdb=" O ASP R 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 134 through 137 removed outlier: 3.595A pdb=" N VAL R 145 " --> pdb=" O ASN R 136 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE R 144 " --> pdb=" O TRP R 156 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG R 154 " --> pdb=" O SER R 146 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL R 153 " --> pdb=" O LEU R 167 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASP R 157 " --> pdb=" O CYS R 163 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N CYS R 163 " --> pdb=" O ASP R 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 174 through 179 removed outlier: 4.220A pdb=" N ALA R 176 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS R 178 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N CYS R 195 " --> pdb=" O THR R 208 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR R 208 " --> pdb=" O CYS R 195 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE R 197 " --> pdb=" O LEU R 206 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 217 through 221 removed outlier: 3.749A pdb=" N PHE R 219 " --> pdb=" O ALA R 232 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA R 232 " --> pdb=" O PHE R 219 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS R 221 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR R 233 " --> pdb=" O THR R 237 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR R 237 " --> pdb=" O THR R 233 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 264 through 267 removed outlier: 3.528A pdb=" N VAL R 275 " --> pdb=" O ASN R 265 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP R 273 " --> pdb=" O SER R 267 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 27 through 32 removed outlier: 4.202A pdb=" N THR N 29 " --> pdb=" O GLY N 42 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR N 31 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA N 40 " --> pdb=" O THR N 31 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS N 60 " --> pdb=" O ILE N 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 69 through 74 removed outlier: 4.161A pdb=" N ILE N 89 " --> pdb=" O SER N 85 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN N 102 " --> pdb=" O GLN N 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 110 through 115 removed outlier: 6.974A pdb=" N CYS N 126 " --> pdb=" O LEU N 111 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL N 113 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU N 124 " --> pdb=" O VAL N 113 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N TYR N 115 " --> pdb=" O LYS N 122 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LYS N 122 " --> pdb=" O TYR N 115 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL N 133 " --> pdb=" O VAL N 125 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS N 141 " --> pdb=" O THR N 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 155 through 159 removed outlier: 4.016A pdb=" N ASN N 170 " --> pdb=" O LYS N 174 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LYS N 174 " --> pdb=" O ASN N 170 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE N 175 " --> pdb=" O SER N 188 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER N 188 " --> pdb=" O ILE N 175 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL N 177 " --> pdb=" O VAL N 186 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 201 through 206 removed outlier: 3.626A pdb=" N ILE N 215 " --> pdb=" O ARG N 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 254 through 259 removed outlier: 4.193A pdb=" N LYS N 256 " --> pdb=" O GLY N 269 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS N 258 " --> pdb=" O VAL N 267 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA N 275 " --> pdb=" O SER N 270 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS N 288 " --> pdb=" O ILE N 278 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU N 280 " --> pdb=" O LEU N 286 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU N 286 " --> pdb=" O GLU N 280 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 298 through 303 removed outlier: 6.666A pdb=" N ILE N 313 " --> pdb=" O LEU N 299 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL N 301 " --> pdb=" O ALA N 311 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA N 311 " --> pdb=" O VAL N 301 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER N 312 " --> pdb=" O SER N 319 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 337 through 338 removed outlier: 6.463A pdb=" N LYS N 337 " --> pdb=" O GLY K5467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'N' and resid 343 through 344 removed outlier: 6.358A pdb=" N VAL N 343 " --> pdb=" O ILE K5430 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'K' and resid 1365 through 1368 removed outlier: 11.332A pdb=" N HIS K5176 " --> pdb=" O ALA K5187 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA K5187 " --> pdb=" O HIS K5176 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N PHE K5178 " --> pdb=" O PHE K5185 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU K5183 " --> pdb=" O ILE K5215 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE K5215 " --> pdb=" O LEU K5183 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N PHE K5185 " --> pdb=" O THR K5213 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR K5213 " --> pdb=" O PHE K5185 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS K5227 " --> pdb=" O ILE K5246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 1395 through 1396 Processing sheet with id=AC9, first strand: chain 'K' and resid 1443 through 1444 Processing sheet with id=AD1, first strand: chain 'K' and resid 1520 through 1522 removed outlier: 3.856A pdb=" N ILE K1521 " --> pdb=" O MET K1530 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET K1530 " --> pdb=" O ILE K1521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'K' and resid 5049 through 5053 removed outlier: 5.218A pdb=" N ASN K5051 " --> pdb=" O VAL K5058 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL K5058 " --> pdb=" O ASN K5051 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP K5053 " --> pdb=" O LEU K5056 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 5070 through 5071 removed outlier: 3.978A pdb=" N TYR K5070 " --> pdb=" O MET K5078 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET K5078 " --> pdb=" O TYR K5070 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'K' and resid 5102 through 5103 Processing sheet with id=AD5, first strand: chain 'K' and resid 5124 through 5125 Processing sheet with id=AD6, first strand: chain 'K' and resid 5399 through 5403 Processing sheet with id=AD7, first strand: chain 'K' and resid 5422 through 5425 removed outlier: 6.625A pdb=" N MET K5422 " --> pdb=" O SER K5498 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER K5498 " --> pdb=" O MET K5422 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE K5424 " --> pdb=" O ILE K5496 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 5474 through 5475 removed outlier: 6.714A pdb=" N ASN K5474 " --> pdb=" O TYR K5510 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'T' and resid 373 through 375 removed outlier: 4.677A pdb=" N LEU T 518 " --> pdb=" O ALA T 346 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA T 510 " --> pdb=" O GLU T 521 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'T' and resid 393 through 394 removed outlier: 4.169A pdb=" N LYS T 393 " --> pdb=" O VAL T 402 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL T 402 " --> pdb=" O LYS T 393 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE T 541 " --> pdb=" O VAL T 552 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL T 552 " --> pdb=" O ILE T 541 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE T 543 " --> pdb=" O GLN T 550 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 407 through 411 Processing sheet with id=AE3, first strand: chain 'T' and resid 467 through 469 731 hydrogen bonds defined for protein. 2073 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 427 hydrogen bonds 854 hydrogen bond angles 0 basepair planarities 165 basepair parallelities 284 stacking parallelities Total time for adding SS restraints: 8.62 Time building geometry restraints manager: 2.36 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: 7317 1.33 - 1.46: 7935 1.46 - 1.58: 12846 1.58 - 1.71: 657 1.71 - 1.83: 162 Bond restraints: 28917 Sorted by residual: bond pdb=" C1' DT J 51 " pdb=" N1 DT J 51 " ideal model delta sigma weight residual 1.468 1.541 -0.073 1.40e-02 5.10e+03 2.70e+01 bond pdb=" C1' DC I 48 " pdb=" N1 DC I 48 " ideal model delta sigma weight residual 1.468 1.540 -0.072 1.40e-02 5.10e+03 2.64e+01 bond pdb=" C1' DT J 96 " pdb=" N1 DT J 96 " ideal model delta sigma weight residual 1.468 1.538 -0.070 1.40e-02 5.10e+03 2.47e+01 bond pdb=" C1' DC J 126 " pdb=" N1 DC J 126 " ideal model delta sigma weight residual 1.468 1.537 -0.069 1.40e-02 5.10e+03 2.43e+01 bond pdb=" C1' DC I 20 " pdb=" N1 DC I 20 " ideal model delta sigma weight residual 1.468 1.536 -0.068 1.40e-02 5.10e+03 2.38e+01 ... (remaining 28912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 39868 3.26 - 6.51: 629 6.51 - 9.77: 43 9.77 - 13.03: 5 13.03 - 16.29: 1 Bond angle restraints: 40546 Sorted by residual: angle pdb=" C4' DT I 50 " pdb=" O4' DT I 50 " pdb=" C1' DT I 50 " ideal model delta sigma weight residual 110.10 104.49 5.61 1.00e+00 1.00e+00 3.15e+01 angle pdb=" CA GLU D 105 " pdb=" CB GLU D 105 " pdb=" CG GLU D 105 " ideal model delta sigma weight residual 114.10 124.47 -10.37 2.00e+00 2.50e-01 2.69e+01 angle pdb=" C4' DG I 147 " pdb=" O4' DG I 147 " pdb=" C1' DG I 147 " ideal model delta sigma weight residual 110.10 105.00 5.10 1.00e+00 1.00e+00 2.60e+01 angle pdb=" CB GLU D 105 " pdb=" CG GLU D 105 " pdb=" CD GLU D 105 " ideal model delta sigma weight residual 112.60 120.79 -8.19 1.70e+00 3.46e-01 2.32e+01 angle pdb=" O4' DA J 68 " pdb=" C1' DA J 68 " pdb=" N9 DA J 68 " ideal model delta sigma weight residual 108.00 111.27 -3.27 7.00e-01 2.04e+00 2.19e+01 ... (remaining 40541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.53: 14050 28.53 - 57.05: 2194 57.05 - 85.58: 246 85.58 - 114.11: 4 114.11 - 142.63: 1 Dihedral angle restraints: 16495 sinusoidal: 8845 harmonic: 7650 Sorted by residual: dihedral pdb=" CA VAL K5381 " pdb=" C VAL K5381 " pdb=" N HIS K5382 " pdb=" CA HIS K5382 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA MET K5280 " pdb=" C MET K5280 " pdb=" N LEU K5281 " pdb=" CA LEU K5281 " ideal model delta harmonic sigma weight residual -180.00 -156.81 -23.19 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA VAL B 43 " pdb=" C VAL B 43 " pdb=" N LYS B 44 " pdb=" CA LYS B 44 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 16492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4068 0.114 - 0.228: 441 0.228 - 0.342: 2 0.342 - 0.456: 0 0.456 - 0.570: 5 Chirality restraints: 4516 Sorted by residual: chirality pdb=" P DA I 146 " pdb=" OP1 DA I 146 " pdb=" OP2 DA I 146 " pdb=" O5' DA I 146 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.12e+00 chirality pdb=" P DC I 145 " pdb=" OP1 DC I 145 " pdb=" OP2 DC I 145 " pdb=" O5' DC I 145 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.57 2.00e-01 2.50e+01 7.99e+00 chirality pdb=" P DG I 148 " pdb=" OP1 DG I 148 " pdb=" OP2 DG I 148 " pdb=" O5' DG I 148 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.34e+00 ... (remaining 4513 not shown) Planarity restraints: 4033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 83 " 0.346 9.50e-02 1.11e+02 1.56e-01 1.66e+01 pdb=" NE ARG A 83 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 83 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 83 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 83 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 128 " 0.337 9.50e-02 1.11e+02 1.51e-01 1.42e+01 pdb=" NE ARG A 128 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 128 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 128 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 128 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " 0.034 2.00e-02 2.50e+03 2.23e-02 9.94e+00 pdb=" CG TYR D 83 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " 0.008 2.00e-02 2.50e+03 ... (remaining 4030 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 12416 2.96 - 3.45: 30043 3.45 - 3.93: 50918 3.93 - 4.42: 58150 4.42 - 4.90: 83282 Nonbonded interactions: 234809 Sorted by model distance: nonbonded pdb=" O5' DA I 146 " pdb=" O4' DA I 146 " model vdw 2.478 2.432 nonbonded pdb=" O ASN C 73 " pdb=" OD1 ASN C 73 " model vdw 2.505 3.040 nonbonded pdb=" O LEU G 65 " pdb=" OD1 ASN G 68 " model vdw 2.539 3.040 nonbonded pdb=" O GLU K5394 " pdb=" OE2 GLU K5394 " model vdw 2.540 3.040 nonbonded pdb=" OE1 GLN E 85 " pdb=" OP1 DG J 69 " model vdw 2.543 3.040 ... (remaining 234804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 19 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } ncs_group { reference = chain 'P' selection = (chain 'Q' and (resid 46 through 98 or (resid 99 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 28.710 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.208 28948 Z= 0.519 Angle : 1.005 20.232 40576 Z= 0.656 Chirality : 0.063 0.570 4516 Planarity : 0.008 0.156 4033 Dihedral : 22.904 142.635 11561 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.59 % Favored : 92.18 % Rotamer: Outliers : 1.85 % Allowed : 19.61 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.16), residues: 2595 helix: -0.81 (0.18), residues: 752 sheet: -2.33 (0.26), residues: 351 loop : -1.64 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 83 TYR 0.050 0.003 TYR D 83 PHE 0.016 0.001 PHE E 104 TRP 0.034 0.002 TRP N 74 HIS 0.018 0.001 HIS K5136 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.52 (28917) covalent geometry : angle 0.98570 / 0.66 (40546) hydrogen bonds : bond 0.16707 / 11.28 ( 1158) hydrogen bonds : angle 7.53192 / 5.35 ( 2927) metal coordination : bond 0.04177 / 2.99 ( 31) metal coordination : angle 7.25861 / 4.59 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 280 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8687 (mm110) cc_final: 0.8457 (mm-40) REVERT: A 65 LEU cc_start: 0.9684 (tp) cc_final: 0.9289 (tt) REVERT: A 115 LYS cc_start: 0.9257 (mmtp) cc_final: 0.9035 (mmtt) REVERT: C 27 VAL cc_start: 0.8258 (t) cc_final: 0.7827 (t) REVERT: C 56 GLU cc_start: 0.8886 (tt0) cc_final: 0.8583 (mt-10) REVERT: D 93 GLU cc_start: 0.9196 (mp0) cc_final: 0.8708 (mp0) REVERT: D 116 LYS cc_start: 0.8949 (ttpp) cc_final: 0.8600 (ttmt) REVERT: E 124 ILE cc_start: 0.9127 (mm) cc_final: 0.8900 (mm) REVERT: F 53 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7669 (tm-30) REVERT: G 110 ASN cc_start: 0.8902 (p0) cc_final: 0.8482 (t0) REVERT: H 35 GLU cc_start: 0.8443 (tp30) cc_final: 0.8206 (tp30) REVERT: H 39 ILE cc_start: 0.8708 (tp) cc_final: 0.8494 (tp) REVERT: H 51 ASP cc_start: 0.7481 (p0) cc_final: 0.7067 (p0) REVERT: H 59 MET cc_start: 0.8510 (tpp) cc_final: 0.8308 (tpp) REVERT: H 93 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7788 (mm-30) REVERT: R 114 TRP cc_start: 0.2859 (m100) cc_final: 0.2619 (m100) REVERT: N 204 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8247 (mp) REVERT: K 5135 MET cc_start: 0.4030 (ptm) cc_final: 0.3572 (pmm) REVERT: K 5177 MET cc_start: 0.4513 (pmm) cc_final: 0.4175 (pmm) REVERT: K 5327 MET cc_start: -0.1995 (tmm) cc_final: -0.2369 (ttt) REVERT: T 500 LYS cc_start: 0.5077 (ptpp) cc_final: 0.4815 (mmtt) REVERT: T 597 MET cc_start: -0.3428 (OUTLIER) cc_final: -0.3923 (ptp) outliers start: 42 outliers final: 23 residues processed: 306 average time/residue: 0.1739 time to fit residues: 83.9982 Evaluate side-chains 261 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain N residue 142 HIS Chi-restraints excluded: chain N residue 204 ILE Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 325 GLN Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 5062 CYS Chi-restraints excluded: chain K residue 5192 LEU Chi-restraints excluded: chain K residue 5417 LEU Chi-restraints excluded: chain T residue 597 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS R 255 HIS ** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 ASN K1377 GLN K1410 ASN K1497 HIS ** K5315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5398 ASN ** K5537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 448 GLN P 94 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.108617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.072439 restraints weight = 132885.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.073864 restraints weight = 68463.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.074037 restraints weight = 43535.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.073893 restraints weight = 39535.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.073622 restraints weight = 35491.107| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 28948 Z= 0.365 Angle : 0.931 11.917 40576 Z= 0.487 Chirality : 0.053 0.267 4516 Planarity : 0.007 0.123 4033 Dihedral : 26.091 141.147 6512 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.36 % Favored : 92.49 % Rotamer: Outliers : 5.69 % Allowed : 18.42 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.15), residues: 2595 helix: -0.68 (0.17), residues: 780 sheet: -2.01 (0.26), residues: 377 loop : -1.68 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 83 TYR 0.042 0.003 TYR F 88 PHE 0.023 0.002 PHE E 67 TRP 0.020 0.002 TRP R 72 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00777 / 0.36 (28917) covalent geometry : angle 0.91953 / 0.49 (40546) hydrogen bonds : bond 0.07627 / 5.19 ( 1158) hydrogen bonds : angle 5.79938 / 4.13 ( 2927) metal coordination : bond 0.01393 / 1.01 ( 31) metal coordination : angle 5.46549 / 3.82 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 222 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8096 (tt) REVERT: A 105 GLU cc_start: 0.8638 (pp20) cc_final: 0.8359 (tm-30) REVERT: A 120 MET cc_start: 0.8314 (mpp) cc_final: 0.7866 (mpp) REVERT: C 73 ASN cc_start: 0.8051 (t0) cc_final: 0.7779 (t0) REVERT: D 71 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8820 (tm-30) REVERT: E 64 LYS cc_start: 0.9072 (ptpp) cc_final: 0.8809 (ptpp) REVERT: F 44 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8531 (tttp) REVERT: G 36 LYS cc_start: 0.8648 (tptt) cc_final: 0.8383 (mmmt) REVERT: H 39 ILE cc_start: 0.9106 (tp) cc_final: 0.8865 (tp) REVERT: H 51 ASP cc_start: 0.7842 (p0) cc_final: 0.7424 (p0) REVERT: H 93 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7875 (mm-30) REVERT: R 75 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6976 (m-80) REVERT: R 114 TRP cc_start: 0.4604 (m100) cc_final: 0.4045 (m100) REVERT: N 73 CYS cc_start: 0.6830 (OUTLIER) cc_final: 0.5771 (m) REVERT: N 167 TYR cc_start: 0.7780 (m-80) cc_final: 0.7473 (m-80) REVERT: N 225 TYR cc_start: 0.8134 (m-80) cc_final: 0.7689 (m-80) REVERT: K 5115 PHE cc_start: 0.5452 (OUTLIER) cc_final: 0.4205 (m-80) REVERT: K 5177 MET cc_start: 0.5677 (pmm) cc_final: 0.5102 (pmm) REVERT: K 5364 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6761 (t80) REVERT: K 5387 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8155 (mp10) REVERT: K 5394 GLU cc_start: 0.8621 (tp30) cc_final: 0.8420 (tp30) REVERT: T 500 LYS cc_start: 0.5143 (ptpp) cc_final: 0.4867 (mmtp) REVERT: T 597 MET cc_start: 0.0009 (OUTLIER) cc_final: -0.0459 (mtt) outliers start: 129 outliers final: 65 residues processed: 327 average time/residue: 0.1608 time to fit residues: 84.2723 Evaluate side-chains 277 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 204 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 75 TYR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 143 VAL Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 5052 LEU Chi-restraints excluded: chain K residue 5062 CYS Chi-restraints excluded: chain K residue 5064 LEU Chi-restraints excluded: chain K residue 5115 PHE Chi-restraints excluded: chain K residue 5184 VAL Chi-restraints excluded: chain K residue 5346 LEU Chi-restraints excluded: chain K residue 5364 TYR Chi-restraints excluded: chain K residue 5387 GLN Chi-restraints excluded: chain K residue 5417 LEU Chi-restraints excluded: chain K residue 5427 ILE Chi-restraints excluded: chain K residue 5476 SER Chi-restraints excluded: chain T residue 428 ASP Chi-restraints excluded: chain T residue 597 MET Chi-restraints excluded: chain P residue 67 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 198 optimal weight: 0.0670 chunk 156 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 277 optimal weight: 20.0000 chunk 214 optimal weight: 6.9990 chunk 217 optimal weight: 0.6980 chunk 244 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 ASN ** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K5315 GLN K5537 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.111590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.075982 restraints weight = 132701.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.077245 restraints weight = 65698.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.077307 restraints weight = 42221.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.077239 restraints weight = 37302.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.077415 restraints weight = 32788.219| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 28948 Z= 0.160 Angle : 0.737 15.716 40576 Z= 0.390 Chirality : 0.047 0.219 4516 Planarity : 0.005 0.097 4033 Dihedral : 26.182 136.299 6496 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.97 % Favored : 93.91 % Rotamer: Outliers : 3.75 % Allowed : 21.07 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.16), residues: 2595 helix: -0.22 (0.18), residues: 776 sheet: -1.75 (0.25), residues: 398 loop : -1.49 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K5266 TYR 0.043 0.002 TYR F 88 PHE 0.021 0.001 PHE E 67 TRP 0.016 0.001 TRP T 421 HIS 0.007 0.001 HIS N 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (28917) covalent geometry : angle 0.72095 / 0.39 (40546) hydrogen bonds : bond 0.04598 / 3.09 ( 1158) hydrogen bonds : angle 5.14123 / 3.66 ( 2927) metal coordination : bond 0.01785 / 1.36 ( 31) metal coordination : angle 5.70126 / 4.53 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 244 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9660 (tp) cc_final: 0.9374 (tp) REVERT: A 73 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8721 (tm-30) REVERT: A 120 MET cc_start: 0.8318 (mpp) cc_final: 0.8089 (mtm) REVERT: B 58 LEU cc_start: 0.9694 (tp) cc_final: 0.9490 (tt) REVERT: C 27 VAL cc_start: 0.8346 (t) cc_final: 0.7922 (t) REVERT: D 40 TYR cc_start: 0.8059 (m-80) cc_final: 0.7836 (m-10) REVERT: D 93 GLU cc_start: 0.9063 (mp0) cc_final: 0.8672 (mp0) REVERT: D 113 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7852 (tm-30) REVERT: D 116 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8724 (ttpp) REVERT: E 41 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.6827 (t80) REVERT: F 44 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8444 (tptt) REVERT: G 36 LYS cc_start: 0.8361 (tptt) cc_final: 0.8100 (mmmt) REVERT: H 39 ILE cc_start: 0.8943 (tp) cc_final: 0.8683 (tp) REVERT: H 51 ASP cc_start: 0.7506 (p0) cc_final: 0.7112 (p0) REVERT: H 105 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7528 (tm-30) REVERT: H 108 LYS cc_start: 0.9214 (pttt) cc_final: 0.8875 (tmmt) REVERT: R 293 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6449 (tp) REVERT: N 265 TYR cc_start: 0.8292 (m-10) cc_final: 0.7957 (m-10) REVERT: N 307 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.7553 (ttp-170) REVERT: N 323 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: K 5115 PHE cc_start: 0.5276 (OUTLIER) cc_final: 0.4154 (m-80) REVERT: K 5177 MET cc_start: 0.5597 (pmm) cc_final: 0.5091 (pmm) REVERT: K 5266 ARG cc_start: 0.8589 (tpp80) cc_final: 0.8245 (ptt-90) REVERT: K 5521 HIS cc_start: 0.8373 (m90) cc_final: 0.8134 (t70) REVERT: T 500 LYS cc_start: 0.5068 (ptpp) cc_final: 0.4825 (mmtt) REVERT: T 597 MET cc_start: -0.0080 (OUTLIER) cc_final: -0.1286 (ptp) outliers start: 85 outliers final: 44 residues processed: 311 average time/residue: 0.1621 time to fit residues: 81.3317 Evaluate side-chains 264 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 214 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 41 TYR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 5052 LEU Chi-restraints excluded: chain K residue 5062 CYS Chi-restraints excluded: chain K residue 5115 PHE Chi-restraints excluded: chain K residue 5184 VAL Chi-restraints excluded: chain K residue 5227 CYS Chi-restraints excluded: chain K residue 5259 SER Chi-restraints excluded: chain K residue 5263 VAL Chi-restraints excluded: chain K residue 5315 GLN Chi-restraints excluded: chain K residue 5345 ILE Chi-restraints excluded: chain K residue 5346 LEU Chi-restraints excluded: chain K residue 5430 ILE Chi-restraints excluded: chain T residue 409 MET Chi-restraints excluded: chain T residue 597 MET Chi-restraints excluded: chain P residue 67 GLN Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 81 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 196 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 chunk 251 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 173 optimal weight: 0.0060 chunk 206 optimal weight: 6.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.111412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.075914 restraints weight = 131913.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.077145 restraints weight = 66200.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.076860 restraints weight = 41942.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.076967 restraints weight = 45087.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.076918 restraints weight = 37698.286| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 28948 Z= 0.157 Angle : 0.711 14.286 40576 Z= 0.374 Chirality : 0.045 0.231 4516 Planarity : 0.004 0.065 4033 Dihedral : 26.278 132.851 6488 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.17 % Favored : 93.72 % Rotamer: Outliers : 4.58 % Allowed : 20.80 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.16), residues: 2595 helix: -0.03 (0.18), residues: 771 sheet: -1.55 (0.26), residues: 383 loop : -1.41 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 83 TYR 0.052 0.002 TYR F 88 PHE 0.020 0.001 PHE E 67 TRP 0.011 0.001 TRP R 114 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (28917) covalent geometry : angle 0.69811 / 0.37 (40546) hydrogen bonds : bond 0.04499 / 3.03 ( 1158) hydrogen bonds : angle 4.87289 / 3.47 ( 2927) metal coordination : bond 0.01230 / 0.90 ( 31) metal coordination : angle 4.92105 / 3.74 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 228 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9670 (tp) cc_final: 0.9383 (tp) REVERT: A 73 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8876 (tm-30) REVERT: A 92 LEU cc_start: 0.9299 (mm) cc_final: 0.8970 (mm) REVERT: A 105 GLU cc_start: 0.8494 (pp20) cc_final: 0.8143 (tm-30) REVERT: A 120 MET cc_start: 0.8366 (mpp) cc_final: 0.8057 (mtm) REVERT: C 27 VAL cc_start: 0.8517 (t) cc_final: 0.8159 (t) REVERT: D 93 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8629 (mp0) REVERT: E 41 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.6914 (t80) REVERT: E 96 CYS cc_start: 0.8424 (p) cc_final: 0.8223 (p) REVERT: F 44 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8202 (tptp) REVERT: G 36 LYS cc_start: 0.8448 (tttt) cc_final: 0.8174 (mmmt) REVERT: H 39 ILE cc_start: 0.8978 (tp) cc_final: 0.8695 (tp) REVERT: H 51 ASP cc_start: 0.7565 (p0) cc_final: 0.7188 (p0) REVERT: H 93 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7679 (mm-30) REVERT: H 105 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7491 (tm-30) REVERT: H 108 LYS cc_start: 0.9211 (pttt) cc_final: 0.8882 (tmmt) REVERT: R 149 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7888 (t80) REVERT: R 266 PHE cc_start: 0.5938 (OUTLIER) cc_final: 0.5698 (m-80) REVERT: N 265 TYR cc_start: 0.8246 (m-10) cc_final: 0.7874 (m-10) REVERT: N 267 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8468 (m) REVERT: N 307 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7691 (ttp-170) REVERT: N 323 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: N 386 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6701 (t80) REVERT: K 5115 PHE cc_start: 0.5571 (OUTLIER) cc_final: 0.4434 (m-80) REVERT: K 5177 MET cc_start: 0.5920 (pmm) cc_final: 0.5473 (pmm) REVERT: K 5389 ARG cc_start: 0.8916 (ptp-170) cc_final: 0.8628 (ptp90) REVERT: K 5521 HIS cc_start: 0.8488 (m90) cc_final: 0.8204 (t-90) REVERT: T 500 LYS cc_start: 0.5132 (ptpp) cc_final: 0.4870 (mmtt) REVERT: T 597 MET cc_start: -0.0034 (mtt) cc_final: -0.1418 (ptp) outliers start: 104 outliers final: 58 residues processed: 309 average time/residue: 0.1551 time to fit residues: 77.5002 Evaluate side-chains 279 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 212 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 41 TYR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 149 PHE Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 266 PHE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain N residue 35 TRP Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain N residue 386 PHE Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 5052 LEU Chi-restraints excluded: chain K residue 5062 CYS Chi-restraints excluded: chain K residue 5108 ARG Chi-restraints excluded: chain K residue 5115 PHE Chi-restraints excluded: chain K residue 5184 VAL Chi-restraints excluded: chain K residue 5227 CYS Chi-restraints excluded: chain K residue 5259 SER Chi-restraints excluded: chain K residue 5263 VAL Chi-restraints excluded: chain K residue 5345 ILE Chi-restraints excluded: chain K residue 5346 LEU Chi-restraints excluded: chain K residue 5417 LEU Chi-restraints excluded: chain K residue 5430 ILE Chi-restraints excluded: chain T residue 409 MET Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain T residue 428 ASP Chi-restraints excluded: chain P residue 67 GLN Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 81 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 24 optimal weight: 0.9990 chunk 259 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 220 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 203 optimal weight: 0.2980 chunk 137 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.112054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3624 r_free = 0.3624 target = 0.074494 restraints weight = 133178.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.076156 restraints weight = 65942.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.076344 restraints weight = 43440.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.076729 restraints weight = 34805.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.076929 restraints weight = 31390.262| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28948 Z= 0.139 Angle : 0.694 12.542 40576 Z= 0.364 Chirality : 0.044 0.257 4516 Planarity : 0.004 0.053 4033 Dihedral : 26.258 131.014 6482 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.90 % Favored : 93.95 % Rotamer: Outliers : 4.05 % Allowed : 21.33 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.16), residues: 2595 helix: 0.05 (0.18), residues: 772 sheet: -1.31 (0.26), residues: 378 loop : -1.37 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 83 TYR 0.056 0.002 TYR F 88 PHE 0.020 0.001 PHE E 67 TRP 0.010 0.001 TRP R 59 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (28917) covalent geometry : angle 0.68332 / 0.36 (40546) hydrogen bonds : bond 0.04097 / 2.75 ( 1158) hydrogen bonds : angle 4.65530 / 3.31 ( 2927) metal coordination : bond 0.01292 / 0.93 ( 31) metal coordination : angle 4.46777 / 3.33 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 230 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9648 (tp) cc_final: 0.9359 (tp) REVERT: A 73 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8789 (tm-30) REVERT: A 92 LEU cc_start: 0.9318 (mm) cc_final: 0.9017 (mm) REVERT: A 94 GLU cc_start: 0.8514 (tp30) cc_final: 0.8107 (tt0) REVERT: A 105 GLU cc_start: 0.8453 (pp20) cc_final: 0.8141 (tm-30) REVERT: A 120 MET cc_start: 0.8307 (mpp) cc_final: 0.7988 (mtm) REVERT: B 44 LYS cc_start: 0.8320 (mtmt) cc_final: 0.7828 (mtmt) REVERT: C 27 VAL cc_start: 0.8453 (t) cc_final: 0.8060 (t) REVERT: D 93 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8709 (mp0) REVERT: E 41 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.6872 (t80) REVERT: F 44 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8665 (mmmt) REVERT: F 81 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8883 (m) REVERT: G 36 LYS cc_start: 0.8449 (tttt) cc_final: 0.8152 (mmmt) REVERT: G 81 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8830 (tpt170) REVERT: H 39 ILE cc_start: 0.8969 (tp) cc_final: 0.8696 (tp) REVERT: H 51 ASP cc_start: 0.7483 (p0) cc_final: 0.7098 (p0) REVERT: H 105 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7397 (tm-30) REVERT: H 108 LYS cc_start: 0.9230 (pttt) cc_final: 0.8953 (tmmt) REVERT: R 149 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7764 (t80) REVERT: R 266 PHE cc_start: 0.5901 (OUTLIER) cc_final: 0.5678 (m-80) REVERT: R 293 ILE cc_start: 0.6515 (OUTLIER) cc_final: 0.5897 (tp) REVERT: N 265 TYR cc_start: 0.8267 (m-10) cc_final: 0.7911 (m-10) REVERT: N 267 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8460 (m) REVERT: N 307 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.7623 (ttp-170) REVERT: N 323 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7744 (mt0) REVERT: N 386 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6910 (t80) REVERT: K 5115 PHE cc_start: 0.5377 (OUTLIER) cc_final: 0.4330 (m-80) REVERT: K 5177 MET cc_start: 0.5713 (pmm) cc_final: 0.5334 (pmm) REVERT: K 5389 ARG cc_start: 0.8980 (ptp-170) cc_final: 0.8665 (ptp90) REVERT: T 500 LYS cc_start: 0.5097 (ptpp) cc_final: 0.4827 (mmtt) REVERT: T 597 MET cc_start: -0.0351 (mtt) cc_final: -0.1625 (ptp) outliers start: 92 outliers final: 56 residues processed: 302 average time/residue: 0.1573 time to fit residues: 76.3486 Evaluate side-chains 282 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 214 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 41 TYR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 81 ARG Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 149 PHE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 266 PHE Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain N residue 35 TRP Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain N residue 386 PHE Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 5052 LEU Chi-restraints excluded: chain K residue 5062 CYS Chi-restraints excluded: chain K residue 5067 THR Chi-restraints excluded: chain K residue 5115 PHE Chi-restraints excluded: chain K residue 5169 ILE Chi-restraints excluded: chain K residue 5227 CYS Chi-restraints excluded: chain K residue 5259 SER Chi-restraints excluded: chain K residue 5263 VAL Chi-restraints excluded: chain K residue 5345 ILE Chi-restraints excluded: chain K residue 5417 LEU Chi-restraints excluded: chain K residue 5430 ILE Chi-restraints excluded: chain K residue 5476 SER Chi-restraints excluded: chain T residue 409 MET Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 81 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 220 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 166 optimal weight: 0.5980 chunk 277 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 267 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.111677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.076125 restraints weight = 133164.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.077212 restraints weight = 66858.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.077646 restraints weight = 45878.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.077632 restraints weight = 40387.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.077388 restraints weight = 34739.173| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28948 Z= 0.144 Angle : 0.676 12.874 40576 Z= 0.357 Chirality : 0.043 0.223 4516 Planarity : 0.004 0.049 4033 Dihedral : 26.317 129.717 6479 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.90 % Favored : 93.99 % Rotamer: Outliers : 3.79 % Allowed : 22.30 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.16), residues: 2595 helix: 0.22 (0.18), residues: 759 sheet: -1.13 (0.27), residues: 364 loop : -1.34 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 35 TYR 0.051 0.002 TYR F 88 PHE 0.021 0.001 PHE E 67 TRP 0.013 0.001 TRP K5535 HIS 0.012 0.001 HIS K5521 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (28917) covalent geometry : angle 0.66858 / 0.36 (40546) hydrogen bonds : bond 0.04131 / 2.77 ( 1158) hydrogen bonds : angle 4.50463 / 3.20 ( 2927) metal coordination : bond 0.01129 / 0.82 ( 31) metal coordination : angle 3.67337 / 2.63 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 223 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8505 (tp30) cc_final: 0.8253 (tt0) REVERT: A 105 GLU cc_start: 0.8489 (pp20) cc_final: 0.8136 (tm-30) REVERT: B 44 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8090 (mtmt) REVERT: B 84 MET cc_start: 0.8102 (tpp) cc_final: 0.7417 (mmp) REVERT: D 93 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8677 (mp0) REVERT: E 41 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.6836 (t80) REVERT: F 81 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8892 (m) REVERT: G 36 LYS cc_start: 0.8558 (tttt) cc_final: 0.8284 (mmmt) REVERT: G 64 GLU cc_start: 0.8121 (tp30) cc_final: 0.7823 (tp30) REVERT: H 39 ILE cc_start: 0.9018 (tp) cc_final: 0.8727 (tp) REVERT: H 51 ASP cc_start: 0.7519 (p0) cc_final: 0.7111 (p0) REVERT: H 59 MET cc_start: 0.8503 (tpp) cc_final: 0.7996 (tpp) REVERT: H 105 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7411 (tm-30) REVERT: H 108 LYS cc_start: 0.9203 (pttt) cc_final: 0.8960 (tmmt) REVERT: R 149 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7861 (t80) REVERT: R 293 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6439 (tp) REVERT: N 242 MET cc_start: 0.8336 (ppp) cc_final: 0.7949 (ppp) REVERT: N 265 TYR cc_start: 0.8333 (m-10) cc_final: 0.7958 (m-10) REVERT: N 267 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8461 (m) REVERT: N 307 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7692 (ttp-170) REVERT: N 323 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: N 386 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6908 (t80) REVERT: K 5105 ASN cc_start: 0.6030 (OUTLIER) cc_final: 0.5406 (m110) REVERT: K 5177 MET cc_start: 0.5860 (pmm) cc_final: 0.5408 (pmm) REVERT: K 5332 MET cc_start: 0.1854 (tpp) cc_final: 0.1476 (tpp) REVERT: K 5364 TYR cc_start: 0.6443 (OUTLIER) cc_final: 0.5869 (t80) REVERT: K 5389 ARG cc_start: 0.8976 (ptp-170) cc_final: 0.8657 (ptp90) REVERT: K 5394 GLU cc_start: 0.8515 (tp30) cc_final: 0.8304 (tm-30) REVERT: T 500 LYS cc_start: 0.5159 (ptpp) cc_final: 0.4864 (mmtt) REVERT: T 597 MET cc_start: -0.0069 (mtt) cc_final: -0.1295 (ptp) outliers start: 86 outliers final: 55 residues processed: 291 average time/residue: 0.1608 time to fit residues: 75.2982 Evaluate side-chains 276 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 211 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 41 TYR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 149 PHE Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain N residue 35 TRP Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain N residue 386 PHE Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 5052 LEU Chi-restraints excluded: chain K residue 5062 CYS Chi-restraints excluded: chain K residue 5105 ASN Chi-restraints excluded: chain K residue 5169 ILE Chi-restraints excluded: chain K residue 5227 CYS Chi-restraints excluded: chain K residue 5259 SER Chi-restraints excluded: chain K residue 5263 VAL Chi-restraints excluded: chain K residue 5344 LYS Chi-restraints excluded: chain K residue 5345 ILE Chi-restraints excluded: chain K residue 5346 LEU Chi-restraints excluded: chain K residue 5364 TYR Chi-restraints excluded: chain K residue 5417 LEU Chi-restraints excluded: chain K residue 5430 ILE Chi-restraints excluded: chain K residue 5476 SER Chi-restraints excluded: chain T residue 409 MET Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain T residue 428 ASP Chi-restraints excluded: chain P residue 66 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 161 optimal weight: 0.6980 chunk 227 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 177 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 232 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 278 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 274 HIS ** K5194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.111677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.073546 restraints weight = 132385.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.075177 restraints weight = 65443.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.075519 restraints weight = 42858.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.076324 restraints weight = 36034.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.076606 restraints weight = 31543.917| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28948 Z= 0.143 Angle : 0.681 13.891 40576 Z= 0.359 Chirality : 0.043 0.255 4516 Planarity : 0.004 0.052 4033 Dihedral : 26.345 129.862 6479 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 3.61 % Allowed : 22.74 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.16), residues: 2595 helix: 0.27 (0.19), residues: 756 sheet: -1.05 (0.27), residues: 366 loop : -1.32 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 128 TYR 0.063 0.002 TYR F 88 PHE 0.018 0.001 PHE E 67 TRP 0.015 0.001 TRP R 59 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (28917) covalent geometry : angle 0.67324 / 0.36 (40546) hydrogen bonds : bond 0.04003 / 2.70 ( 1158) hydrogen bonds : angle 4.42874 / 3.14 ( 2927) metal coordination : bond 0.01022 / 0.73 ( 31) metal coordination : angle 3.91170 / 2.83 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 227 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8548 (tm-30) REVERT: A 94 GLU cc_start: 0.8421 (tp30) cc_final: 0.8111 (tt0) REVERT: A 105 GLU cc_start: 0.8490 (pp20) cc_final: 0.8155 (tm-30) REVERT: B 44 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8117 (mtmt) REVERT: B 84 MET cc_start: 0.7947 (tpp) cc_final: 0.7651 (tpp) REVERT: B 88 TYR cc_start: 0.7475 (m-80) cc_final: 0.7121 (m-80) REVERT: D 93 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8705 (mp0) REVERT: E 41 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.6820 (t80) REVERT: F 39 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.6527 (mpp80) REVERT: F 44 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8372 (tptp) REVERT: F 81 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8895 (m) REVERT: G 36 LYS cc_start: 0.8574 (tttt) cc_final: 0.8324 (mmmt) REVERT: H 39 ILE cc_start: 0.9077 (tp) cc_final: 0.8817 (tp) REVERT: H 43 LYS cc_start: 0.9313 (mptt) cc_final: 0.8847 (ttmm) REVERT: H 51 ASP cc_start: 0.7526 (p0) cc_final: 0.7105 (p0) REVERT: H 108 LYS cc_start: 0.9206 (pttt) cc_final: 0.8976 (tmmt) REVERT: R 149 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7682 (t80) REVERT: R 211 ASP cc_start: 0.4918 (t0) cc_final: 0.4395 (p0) REVERT: R 238 LEU cc_start: 0.7431 (tt) cc_final: 0.7215 (mt) REVERT: R 293 ILE cc_start: 0.6501 (OUTLIER) cc_final: 0.5948 (tp) REVERT: N 242 MET cc_start: 0.8382 (ppp) cc_final: 0.7960 (ppp) REVERT: N 265 TYR cc_start: 0.8390 (m-10) cc_final: 0.8051 (m-10) REVERT: N 267 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8507 (m) REVERT: N 307 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.7642 (ttp-170) REVERT: N 323 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7649 (mt0) REVERT: N 386 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6917 (t80) REVERT: K 5115 PHE cc_start: 0.5407 (OUTLIER) cc_final: 0.4286 (m-80) REVERT: K 5177 MET cc_start: 0.5610 (pmm) cc_final: 0.5267 (pmm) REVERT: K 5332 MET cc_start: 0.1730 (tpp) cc_final: 0.1400 (tpp) REVERT: K 5364 TYR cc_start: 0.6413 (OUTLIER) cc_final: 0.5986 (t80) REVERT: K 5389 ARG cc_start: 0.8955 (ptp-170) cc_final: 0.8635 (ptp90) REVERT: K 5452 MET cc_start: 0.8016 (mpp) cc_final: 0.7088 (mtt) REVERT: K 5499 SER cc_start: 0.7189 (OUTLIER) cc_final: 0.6382 (p) REVERT: T 500 LYS cc_start: 0.5170 (ptpp) cc_final: 0.4838 (mmtt) REVERT: T 597 MET cc_start: -0.0429 (mtt) cc_final: -0.1521 (ptp) outliers start: 82 outliers final: 55 residues processed: 296 average time/residue: 0.1655 time to fit residues: 79.3667 Evaluate side-chains 279 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 212 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 41 TYR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 149 PHE Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain N residue 35 TRP Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain N residue 386 PHE Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 5052 LEU Chi-restraints excluded: chain K residue 5062 CYS Chi-restraints excluded: chain K residue 5115 PHE Chi-restraints excluded: chain K residue 5169 ILE Chi-restraints excluded: chain K residue 5227 CYS Chi-restraints excluded: chain K residue 5259 SER Chi-restraints excluded: chain K residue 5263 VAL Chi-restraints excluded: chain K residue 5344 LYS Chi-restraints excluded: chain K residue 5345 ILE Chi-restraints excluded: chain K residue 5364 TYR Chi-restraints excluded: chain K residue 5417 LEU Chi-restraints excluded: chain K residue 5430 ILE Chi-restraints excluded: chain K residue 5476 SER Chi-restraints excluded: chain K residue 5497 ILE Chi-restraints excluded: chain K residue 5499 SER Chi-restraints excluded: chain T residue 409 MET Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain T residue 428 ASP Chi-restraints excluded: chain T residue 536 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 133 optimal weight: 7.9990 chunk 198 optimal weight: 0.0270 chunk 249 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 237 optimal weight: 0.0770 chunk 172 optimal weight: 8.9990 overall best weight: 0.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 136 ASN ** R 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.112362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.077691 restraints weight = 133618.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.077349 restraints weight = 74237.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.078302 restraints weight = 48071.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.078033 restraints weight = 35448.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.078034 restraints weight = 34482.796| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28948 Z= 0.131 Angle : 0.677 14.385 40576 Z= 0.357 Chirality : 0.043 0.219 4516 Planarity : 0.004 0.048 4033 Dihedral : 26.302 130.190 6478 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 3.48 % Allowed : 23.31 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.16), residues: 2595 helix: 0.27 (0.19), residues: 765 sheet: -0.97 (0.26), residues: 376 loop : -1.32 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 128 TYR 0.057 0.002 TYR F 88 PHE 0.018 0.001 PHE E 67 TRP 0.014 0.001 TRP R 59 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (28917) covalent geometry : angle 0.67085 / 0.36 (40546) hydrogen bonds : bond 0.03807 / 2.57 ( 1158) hydrogen bonds : angle 4.31325 / 3.07 ( 2927) metal coordination : bond 0.01098 / 0.78 ( 31) metal coordination : angle 3.52916 / 2.52 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 236 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8566 (tm-30) REVERT: A 105 GLU cc_start: 0.8478 (pp20) cc_final: 0.8115 (tm-30) REVERT: B 44 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8155 (mtmt) REVERT: D 93 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8676 (mp0) REVERT: E 41 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.6782 (t80) REVERT: F 39 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.6555 (mpp80) REVERT: F 81 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8849 (m) REVERT: G 36 LYS cc_start: 0.8525 (tttt) cc_final: 0.8276 (mmmt) REVERT: H 39 ILE cc_start: 0.9056 (tp) cc_final: 0.8846 (tp) REVERT: H 43 LYS cc_start: 0.9286 (mptt) cc_final: 0.8934 (mttp) REVERT: H 51 ASP cc_start: 0.7544 (p0) cc_final: 0.7143 (p0) REVERT: H 59 MET cc_start: 0.8223 (tpp) cc_final: 0.7566 (tpp) REVERT: H 105 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7287 (tm-30) REVERT: R 149 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7903 (t80) REVERT: R 211 ASP cc_start: 0.4873 (t0) cc_final: 0.4382 (p0) REVERT: R 238 LEU cc_start: 0.7601 (tt) cc_final: 0.7395 (mt) REVERT: N 242 MET cc_start: 0.8350 (ppp) cc_final: 0.7947 (ppp) REVERT: N 265 TYR cc_start: 0.8439 (m-10) cc_final: 0.8101 (m-10) REVERT: N 267 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8461 (m) REVERT: N 307 ARG cc_start: 0.8120 (ttp-170) cc_final: 0.7694 (ttp-170) REVERT: N 323 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7641 (mt0) REVERT: N 386 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6862 (t80) REVERT: K 5115 PHE cc_start: 0.5641 (OUTLIER) cc_final: 0.4385 (m-80) REVERT: K 5177 MET cc_start: 0.5883 (pmm) cc_final: 0.5485 (pmm) REVERT: K 5327 MET cc_start: -0.1144 (tmm) cc_final: -0.1883 (tpt) REVERT: K 5332 MET cc_start: 0.2095 (tpp) cc_final: 0.1753 (tpp) REVERT: K 5364 TYR cc_start: 0.6419 (OUTLIER) cc_final: 0.5871 (t80) REVERT: K 5387 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8140 (mp10) REVERT: K 5389 ARG cc_start: 0.8965 (ptp-170) cc_final: 0.8688 (ptp90) REVERT: K 5394 GLU cc_start: 0.8582 (tp30) cc_final: 0.8357 (tm-30) REVERT: K 5452 MET cc_start: 0.8004 (mpp) cc_final: 0.7368 (mmm) REVERT: K 5499 SER cc_start: 0.6928 (OUTLIER) cc_final: 0.6201 (p) REVERT: T 500 LYS cc_start: 0.5063 (ptpp) cc_final: 0.4742 (mmtt) REVERT: T 597 MET cc_start: -0.0392 (mtt) cc_final: -0.1511 (ptp) outliers start: 79 outliers final: 54 residues processed: 299 average time/residue: 0.1634 time to fit residues: 78.6393 Evaluate side-chains 284 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 218 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 41 TYR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 149 PHE Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain N residue 35 TRP Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain N residue 386 PHE Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 5052 LEU Chi-restraints excluded: chain K residue 5062 CYS Chi-restraints excluded: chain K residue 5088 LEU Chi-restraints excluded: chain K residue 5115 PHE Chi-restraints excluded: chain K residue 5169 ILE Chi-restraints excluded: chain K residue 5259 SER Chi-restraints excluded: chain K residue 5263 VAL Chi-restraints excluded: chain K residue 5344 LYS Chi-restraints excluded: chain K residue 5345 ILE Chi-restraints excluded: chain K residue 5346 LEU Chi-restraints excluded: chain K residue 5364 TYR Chi-restraints excluded: chain K residue 5387 GLN Chi-restraints excluded: chain K residue 5417 LEU Chi-restraints excluded: chain K residue 5430 ILE Chi-restraints excluded: chain K residue 5476 SER Chi-restraints excluded: chain K residue 5499 SER Chi-restraints excluded: chain T residue 376 CYS Chi-restraints excluded: chain T residue 409 MET Chi-restraints excluded: chain T residue 410 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 91 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 224 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 251 optimal weight: 0.0870 chunk 197 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 240 optimal weight: 3.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.111952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.075809 restraints weight = 132839.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.075658 restraints weight = 66939.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.076015 restraints weight = 42944.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.076858 restraints weight = 35433.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.077084 restraints weight = 31147.577| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28948 Z= 0.140 Angle : 0.689 13.984 40576 Z= 0.360 Chirality : 0.043 0.219 4516 Planarity : 0.004 0.051 4033 Dihedral : 26.338 130.134 6478 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 3.26 % Allowed : 23.49 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.16), residues: 2595 helix: 0.32 (0.19), residues: 763 sheet: -0.93 (0.27), residues: 366 loop : -1.29 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 33 TYR 0.056 0.002 TYR F 88 PHE 0.017 0.001 PHE E 67 TRP 0.016 0.001 TRP R 59 HIS 0.007 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (28917) covalent geometry : angle 0.68091 / 0.36 (40546) hydrogen bonds : bond 0.03869 / 2.59 ( 1158) hydrogen bonds : angle 4.27864 / 3.04 ( 2927) metal coordination : bond 0.01021 / 0.73 ( 31) metal coordination : angle 3.83051 / 2.74 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 217 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8546 (tm-30) REVERT: A 105 GLU cc_start: 0.8498 (pp20) cc_final: 0.8124 (tm-30) REVERT: B 44 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8220 (mtmt) REVERT: D 93 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8714 (mp0) REVERT: E 41 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.6796 (t80) REVERT: F 39 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.6487 (mpp80) REVERT: F 81 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8825 (m) REVERT: G 36 LYS cc_start: 0.8619 (tttt) cc_final: 0.8368 (mmmt) REVERT: H 39 ILE cc_start: 0.9142 (tp) cc_final: 0.8890 (tp) REVERT: H 43 LYS cc_start: 0.9307 (mptt) cc_final: 0.9000 (mttp) REVERT: H 51 ASP cc_start: 0.7638 (p0) cc_final: 0.7236 (p0) REVERT: R 149 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7771 (t80) REVERT: R 211 ASP cc_start: 0.4924 (t0) cc_final: 0.4538 (p0) REVERT: R 243 TYR cc_start: 0.7015 (p90) cc_final: 0.6428 (p90) REVERT: N 242 MET cc_start: 0.8368 (ppp) cc_final: 0.7902 (ppp) REVERT: N 265 TYR cc_start: 0.8420 (m-10) cc_final: 0.8085 (m-10) REVERT: N 267 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8466 (m) REVERT: N 323 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7527 (mt0) REVERT: K 1478 MET cc_start: 0.4059 (mmm) cc_final: 0.3784 (mmt) REVERT: K 5115 PHE cc_start: 0.5610 (OUTLIER) cc_final: 0.4343 (m-80) REVERT: K 5177 MET cc_start: 0.5810 (pmm) cc_final: 0.5445 (pmm) REVERT: K 5332 MET cc_start: 0.2093 (tpp) cc_final: 0.1757 (tpp) REVERT: K 5364 TYR cc_start: 0.6454 (OUTLIER) cc_final: 0.6033 (t80) REVERT: K 5387 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8176 (mp10) REVERT: K 5389 ARG cc_start: 0.8974 (ptp-170) cc_final: 0.8739 (ptp90) REVERT: K 5452 MET cc_start: 0.7975 (mpp) cc_final: 0.7333 (mmm) REVERT: K 5499 SER cc_start: 0.7105 (OUTLIER) cc_final: 0.6353 (p) REVERT: T 500 LYS cc_start: 0.4994 (ptpp) cc_final: 0.4666 (mmtt) REVERT: T 597 MET cc_start: -0.0873 (mtt) cc_final: -0.2079 (ptp) outliers start: 74 outliers final: 54 residues processed: 271 average time/residue: 0.1717 time to fit residues: 75.1320 Evaluate side-chains 272 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 41 TYR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 149 PHE Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain N residue 35 TRP Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 5052 LEU Chi-restraints excluded: chain K residue 5062 CYS Chi-restraints excluded: chain K residue 5088 LEU Chi-restraints excluded: chain K residue 5115 PHE Chi-restraints excluded: chain K residue 5169 ILE Chi-restraints excluded: chain K residue 5227 CYS Chi-restraints excluded: chain K residue 5259 SER Chi-restraints excluded: chain K residue 5263 VAL Chi-restraints excluded: chain K residue 5344 LYS Chi-restraints excluded: chain K residue 5345 ILE Chi-restraints excluded: chain K residue 5346 LEU Chi-restraints excluded: chain K residue 5364 TYR Chi-restraints excluded: chain K residue 5387 GLN Chi-restraints excluded: chain K residue 5417 LEU Chi-restraints excluded: chain K residue 5476 SER Chi-restraints excluded: chain K residue 5497 ILE Chi-restraints excluded: chain K residue 5499 SER Chi-restraints excluded: chain T residue 409 MET Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain T residue 536 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 284 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 142 optimal weight: 0.0000 chunk 124 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 252 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1493 ASN K1497 HIS ** K5356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.110831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.073782 restraints weight = 132807.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.074326 restraints weight = 65078.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.075105 restraints weight = 42815.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.075591 restraints weight = 34897.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.075693 restraints weight = 31459.499| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 28948 Z= 0.162 Angle : 0.698 13.517 40576 Z= 0.366 Chirality : 0.043 0.219 4516 Planarity : 0.004 0.049 4033 Dihedral : 26.454 130.265 6478 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.55 % Favored : 93.37 % Rotamer: Outliers : 2.73 % Allowed : 24.28 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.16), residues: 2595 helix: 0.32 (0.19), residues: 763 sheet: -0.93 (0.26), residues: 369 loop : -1.29 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 116 TYR 0.056 0.002 TYR F 88 PHE 0.024 0.001 PHE N 386 TRP 0.052 0.002 TRP T 421 HIS 0.006 0.001 HIS R 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (28917) covalent geometry : angle 0.69014 / 0.37 (40546) hydrogen bonds : bond 0.04091 / 2.76 ( 1158) hydrogen bonds : angle 4.28227 / 3.05 ( 2927) metal coordination : bond 0.01073 / 0.77 ( 31) metal coordination : angle 3.91504 / 2.74 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8732 (tm-30) REVERT: A 105 GLU cc_start: 0.8526 (pp20) cc_final: 0.8216 (tm-30) REVERT: D 89 ILE cc_start: 0.8969 (mt) cc_final: 0.8642 (mp) REVERT: D 93 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8710 (mp0) REVERT: E 41 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.6848 (t80) REVERT: F 39 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.6430 (mpp80) REVERT: F 81 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.8910 (m) REVERT: G 36 LYS cc_start: 0.8682 (tttt) cc_final: 0.8441 (mmmt) REVERT: H 39 ILE cc_start: 0.9112 (tp) cc_final: 0.8842 (tp) REVERT: H 43 LYS cc_start: 0.9299 (mptt) cc_final: 0.8863 (ttmm) REVERT: H 51 ASP cc_start: 0.7794 (p0) cc_final: 0.7417 (p0) REVERT: R 149 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7738 (t80) REVERT: R 211 ASP cc_start: 0.5020 (t0) cc_final: 0.4585 (p0) REVERT: R 243 TYR cc_start: 0.7057 (p90) cc_final: 0.6460 (p90) REVERT: N 242 MET cc_start: 0.8408 (ppp) cc_final: 0.7955 (ppp) REVERT: N 265 TYR cc_start: 0.8450 (m-10) cc_final: 0.8141 (m-10) REVERT: N 267 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8538 (m) REVERT: N 323 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7503 (mt0) REVERT: K 1478 MET cc_start: 0.4296 (mmm) cc_final: 0.4089 (mmt) REVERT: K 5115 PHE cc_start: 0.5567 (OUTLIER) cc_final: 0.4290 (m-80) REVERT: K 5177 MET cc_start: 0.5657 (pmm) cc_final: 0.5288 (pmm) REVERT: K 5332 MET cc_start: 0.2172 (tpp) cc_final: 0.1852 (tpp) REVERT: K 5364 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.6030 (t80) REVERT: K 5387 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8172 (mp10) REVERT: K 5389 ARG cc_start: 0.8986 (ptp-170) cc_final: 0.8763 (ptm160) REVERT: K 5452 MET cc_start: 0.7983 (mpp) cc_final: 0.7350 (mmm) REVERT: K 5499 SER cc_start: 0.7242 (OUTLIER) cc_final: 0.6453 (p) REVERT: T 500 LYS cc_start: 0.5048 (ptpp) cc_final: 0.4708 (mmtt) outliers start: 62 outliers final: 49 residues processed: 263 average time/residue: 0.1697 time to fit residues: 71.4272 Evaluate side-chains 270 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 41 TYR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 149 PHE Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain N residue 35 TRP Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 5052 LEU Chi-restraints excluded: chain K residue 5062 CYS Chi-restraints excluded: chain K residue 5088 LEU Chi-restraints excluded: chain K residue 5115 PHE Chi-restraints excluded: chain K residue 5169 ILE Chi-restraints excluded: chain K residue 5227 CYS Chi-restraints excluded: chain K residue 5259 SER Chi-restraints excluded: chain K residue 5344 LYS Chi-restraints excluded: chain K residue 5345 ILE Chi-restraints excluded: chain K residue 5346 LEU Chi-restraints excluded: chain K residue 5364 TYR Chi-restraints excluded: chain K residue 5387 GLN Chi-restraints excluded: chain K residue 5417 LEU Chi-restraints excluded: chain K residue 5476 SER Chi-restraints excluded: chain K residue 5497 ILE Chi-restraints excluded: chain K residue 5499 SER Chi-restraints excluded: chain T residue 409 MET Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain T residue 536 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 127 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 231 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 283 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1493 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.110410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.073955 restraints weight = 133188.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.074079 restraints weight = 64899.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.074873 restraints weight = 42664.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.075510 restraints weight = 34202.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.075661 restraints weight = 30455.425| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 28948 Z= 0.161 Angle : 0.703 13.920 40576 Z= 0.367 Chirality : 0.043 0.219 4516 Planarity : 0.004 0.051 4033 Dihedral : 26.513 130.811 6478 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 3.00 % Allowed : 23.93 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.16), residues: 2595 helix: 0.25 (0.19), residues: 778 sheet: -0.93 (0.26), residues: 373 loop : -1.30 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 116 TYR 0.059 0.002 TYR F 88 PHE 0.015 0.001 PHE E 67 TRP 0.032 0.002 TRP T 421 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (28917) covalent geometry : angle 0.69527 / 0.37 (40546) hydrogen bonds : bond 0.03939 / 2.65 ( 1158) hydrogen bonds : angle 4.27690 / 3.03 ( 2927) metal coordination : bond 0.01034 / 0.74 ( 31) metal coordination : angle 3.82380 / 2.72 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5906.62 seconds wall clock time: 102 minutes 4.75 seconds (6124.75 seconds total)