Starting phenix.real_space_refine on Sun Jul 5 13:32:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yly_73097/07_2026/9yly_73097.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yly_73097/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9yly_73097/07_2026/9yly_73097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yly_73097/07_2026/9yly_73097.map" model { file = "/net/cci-nas-00/data/ceres_data/9yly_73097/07_2026/9yly_73097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yly_73097/07_2026/9yly_73097.cif" } 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-dev-6108/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: 5.39, per 1000 atoms: 0.19 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: 2.72 Conformation dependent library (CDL) restraints added in 678.8 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: 3.24 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: 8.26 Time building geometry restraints manager: 3.22 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: 39870 3.26 - 6.51: 627 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: 2.480 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 32.080 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.700 ------------------------------------------------------------------------------- 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 : 1.002 20.232 40576 Z= 0.654 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 0.98316 / 0.65 (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 : 0.735 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: 0.8456 (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: 0.7825 (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: 0.8709 (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: 0.8899 (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: 0.8483 (t0) REVERT: H 35 GLU cc_start: 0.8443 (tp30) cc_final: 0.8207 (tp30) REVERT: H 39 ILE cc_start: 0.8708 (tp) cc_final: 0.8498 (tp) REVERT: H 51 ASP cc_start: 0.7481 (p0) cc_final: 0.7066 (p0) REVERT: H 59 MET cc_start: 0.8510 (tpp) cc_final: 0.8309 (tpp) REVERT: H 93 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7790 (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: -0.2370 (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: -0.3922 (ptp) outliers start: 42 outliers final: 23 residues processed: 306 average time/residue: 0.1922 time to fit residues: 91.9127 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 : 0.904 ------------------------------------------------------------------------------- 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: 0.6980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 T 448 GLN P 94 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.107543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.069607 restraints weight = 132240.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.070744 restraints weight = 66485.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.071417 restraints weight = 44682.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.071786 restraints weight = 36505.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.071999 restraints weight = 32880.135| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 28948 Z= 0.397 Angle : 0.962 11.907 40576 Z= 0.511 Chirality : 0.054 0.288 4516 Planarity : 0.007 0.131 4033 Dihedral : 26.381 142.116 6512 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.67 % Favored : 92.14 % Rotamer: Outliers : 6.26 % Allowed : 18.60 % Favored : 75.14 % 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: -2.27 (0.15), residues: 2595 helix: -0.85 (0.17), residues: 788 sheet: -2.16 (0.25), residues: 390 loop : -1.68 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 83 TYR 0.059 0.003 TYR F 88 PHE 0.022 0.003 PHE E 67 TRP 0.018 0.002 TRP R 156 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00838 / 0.40 (28917) covalent geometry : angle 0.94961 / 0.51 (40546) hydrogen bonds : bond 0.08402 / 5.74 ( 1158) hydrogen bonds : angle 5.97464 / 4.25 ( 2927) metal coordination : bond 0.01634 / 1.18 ( 31) metal coordination : angle 5.71646 / 4.02 ( 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 359 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 217 time to evaluate : 0.894 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 105 GLU cc_start: 0.8645 (pp20) cc_final: 0.8341 (tm-30) REVERT: A 120 MET cc_start: 0.8305 (mpp) cc_final: 0.7858 (mpp) REVERT: C 73 ASN cc_start: 0.7947 (t0) cc_final: 0.7679 (t0) REVERT: D 71 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8824 (tm-30) REVERT: D 95 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8691 (tm-30) REVERT: D 99 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.8234 (ttp-110) REVERT: E 64 LYS cc_start: 0.8955 (ptpp) cc_final: 0.8690 (ptpp) REVERT: E 92 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8998 (mm) REVERT: F 44 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8456 (tttp) REVERT: G 36 LYS cc_start: 0.8731 (tptt) cc_final: 0.8498 (mmmt) REVERT: H 39 ILE cc_start: 0.9170 (tp) cc_final: 0.8932 (tp) REVERT: H 51 ASP cc_start: 0.7897 (p0) cc_final: 0.7414 (p0) REVERT: H 93 GLU cc_start: 0.8526 (mm-30) cc_final: 0.7886 (mm-30) REVERT: R 75 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6835 (m-80) REVERT: R 114 TRP cc_start: 0.4747 (m100) cc_final: 0.3988 (m100) REVERT: R 211 ASP cc_start: 0.6206 (p0) cc_final: 0.5950 (p0) REVERT: R 293 ILE cc_start: 0.6583 (OUTLIER) cc_final: 0.5960 (tp) REVERT: N 73 CYS cc_start: 0.6941 (OUTLIER) cc_final: 0.5689 (m) REVERT: N 128 MET cc_start: 0.7176 (mtp) cc_final: 0.6955 (mtp) REVERT: N 225 TYR cc_start: 0.8172 (m-80) cc_final: 0.7785 (m-80) REVERT: N 265 TYR cc_start: 0.8251 (m-10) cc_final: 0.7787 (m-10) REVERT: K 5115 PHE cc_start: 0.5324 (OUTLIER) cc_final: 0.4169 (m-80) REVERT: K 5177 MET cc_start: 0.5648 (pmm) cc_final: 0.5105 (pmm) REVERT: K 5364 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6730 (t80) REVERT: T 500 LYS cc_start: 0.5164 (ptpp) cc_final: 0.4898 (mmtp) REVERT: T 597 MET cc_start: -0.0746 (OUTLIER) cc_final: -0.1171 (mtt) outliers start: 142 outliers final: 69 residues processed: 334 average time/residue: 0.1760 time to fit residues: 93.6667 Evaluate side-chains 276 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 198 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 95 GLN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 92 LEU 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 71 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 85 ASP 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 R residue 293 ILE 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 325 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 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 5399 VAL 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 597 MET Chi-restraints excluded: chain P residue 67 GLN Chi-restraints excluded: chain Q residue 47 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 198 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 277 optimal weight: 20.0000 chunk 214 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** G 31 HIS R 178 HIS R 225 ASN ** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K5315 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.111332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.076075 restraints weight = 132294.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.076269 restraints weight = 67337.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.076604 restraints weight = 49016.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.076808 restraints weight = 36306.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.076706 restraints weight = 33847.260| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2192 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= 0.155 Angle : 0.738 15.788 40576 Z= 0.391 Chirality : 0.047 0.228 4516 Planarity : 0.005 0.098 4033 Dihedral : 26.370 137.473 6499 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.93 % Favored : 93.91 % Rotamer: Outliers : 4.19 % Allowed : 20.67 % Favored : 75.14 % 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: -1.77 (0.16), residues: 2595 helix: -0.26 (0.18), residues: 780 sheet: -1.82 (0.25), residues: 390 loop : -1.50 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG K5266 TYR 0.035 0.002 TYR F 88 PHE 0.021 0.002 PHE E 67 TRP 0.017 0.001 TRP T 421 HIS 0.007 0.001 HIS N 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (28917) covalent geometry : angle 0.71960 / 0.39 (40546) hydrogen bonds : bond 0.04600 / 3.09 ( 1158) hydrogen bonds : angle 5.17533 / 3.68 ( 2927) metal coordination : bond 0.01702 / 1.28 ( 31) metal coordination : angle 5.98820 / 4.67 ( 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 343 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 248 time to evaluate : 0.942 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: 0.9652 (tp) cc_final: 0.9361 (tp) REVERT: A 73 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 105 GLU cc_start: 0.8587 (pp20) cc_final: 0.8235 (tm-30) REVERT: A 120 MET cc_start: 0.8354 (mpp) cc_final: 0.8127 (mtm) REVERT: C 27 VAL cc_start: 0.8391 (t) cc_final: 0.7969 (t) REVERT: D 86 ARG cc_start: 0.7938 (mmp80) cc_final: 0.7627 (mmp80) REVERT: D 93 GLU cc_start: 0.9062 (mp0) cc_final: 0.8678 (mp0) REVERT: D 95 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8769 (tt0) REVERT: E 41 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.6892 (t80) REVERT: E 64 LYS cc_start: 0.8981 (ptpp) cc_final: 0.8724 (ptpp) REVERT: G 36 LYS cc_start: 0.8444 (tptt) cc_final: 0.8167 (mmmt) REVERT: H 39 ILE cc_start: 0.8994 (tp) cc_final: 0.8719 (tp) REVERT: H 51 ASP cc_start: 0.7474 (p0) cc_final: 0.7058 (p0) REVERT: H 105 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7542 (tm-30) REVERT: H 108 LYS cc_start: 0.9217 (pttt) cc_final: 0.8881 (tmmt) REVERT: R 149 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7877 (t80) REVERT: N 242 MET cc_start: 0.8165 (ppp) cc_final: 0.7862 (ppp) REVERT: N 265 TYR cc_start: 0.8343 (m-10) cc_final: 0.8034 (m-10) REVERT: N 267 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8629 (m) REVERT: N 307 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.7536 (ttp-170) REVERT: N 323 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7758 (mt0) REVERT: K 5115 PHE cc_start: 0.5284 (OUTLIER) cc_final: 0.4155 (m-80) REVERT: K 5177 MET cc_start: 0.5630 (pmm) cc_final: 0.5115 (pmm) REVERT: K 5266 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8252 (ptt-90) REVERT: K 5331 LEU cc_start: 0.4591 (OUTLIER) cc_final: 0.4383 (mm) REVERT: K 5332 MET cc_start: 0.1621 (tpp) cc_final: 0.1323 (tpp) REVERT: K 5389 ARG cc_start: 0.8924 (ptp-170) cc_final: 0.8675 (ptp90) REVERT: K 5452 MET cc_start: 0.8087 (mpp) cc_final: 0.7295 (mtm) REVERT: T 500 LYS cc_start: 0.5117 (ptpp) cc_final: 0.4863 (mmtt) REVERT: T 597 MET cc_start: -0.0211 (OUTLIER) cc_final: -0.1397 (ptp) outliers start: 95 outliers final: 50 residues processed: 319 average time/residue: 0.1899 time to fit residues: 96.3582 Evaluate side-chains 274 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 49 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU 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 95 GLN 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 96 CYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 59 THR 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 H residue 100 LEU 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 175 SER Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 301 THR 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 267 VAL Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain N residue 325 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 5263 VAL Chi-restraints excluded: chain K residue 5315 GLN Chi-restraints excluded: chain K residue 5331 LEU 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 428 ASP 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: 0.9990 chunk 130 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 266 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 7 optimal weight: 0.0980 chunk 215 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 173 optimal weight: 30.0000 chunk 206 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5356 ASN ** 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 = 0.4228 r_free = 0.4228 target = 0.109953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.071773 restraints weight = 131866.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.073275 restraints weight = 65837.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.073658 restraints weight = 44206.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.074100 restraints weight = 35937.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.074204 restraints weight = 32336.625| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 28948 Z= 0.189 Angle : 0.720 13.013 40576 Z= 0.383 Chirality : 0.045 0.210 4516 Planarity : 0.005 0.063 4033 Dihedral : 26.532 133.922 6491 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.59 % Favored : 93.26 % Rotamer: Outliers : 4.85 % Allowed : 20.67 % Favored : 74.48 % 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: -1.63 (0.16), residues: 2595 helix: -0.09 (0.18), residues: 774 sheet: -1.61 (0.26), residues: 379 loop : -1.49 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 83 TYR 0.049 0.002 TYR F 88 PHE 0.020 0.001 PHE E 67 TRP 0.013 0.001 TRP N 321 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (28917) covalent geometry : angle 0.70825 / 0.38 (40546) hydrogen bonds : bond 0.04907 / 3.32 ( 1158) hydrogen bonds : angle 4.98392 / 3.55 ( 2927) metal coordination : bond 0.01270 / 0.92 ( 31) metal coordination : angle 4.91486 / 3.64 ( 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: 110 poor density : 222 time to evaluate : 0.918 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 65 LEU cc_start: 0.9703 (tp) cc_final: 0.9415 (tp) REVERT: A 73 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8738 (tm-30) REVERT: A 94 GLU cc_start: 0.8606 (tp30) cc_final: 0.8401 (tt0) REVERT: A 105 GLU cc_start: 0.8515 (pp20) cc_final: 0.8305 (tm-30) REVERT: A 120 MET cc_start: 0.8347 (mpp) cc_final: 0.8041 (mtm) REVERT: B 44 LYS cc_start: 0.8725 (mtpt) cc_final: 0.8354 (ttmt) REVERT: C 27 VAL cc_start: 0.8587 (t) cc_final: 0.8242 (t) REVERT: D 93 GLU cc_start: 0.9116 (mp0) cc_final: 0.8652 (mp0) REVERT: E 41 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.6917 (t80) REVERT: E 64 LYS cc_start: 0.8897 (ptpp) cc_final: 0.8620 (ptpp) REVERT: G 36 LYS cc_start: 0.8647 (tttt) cc_final: 0.8394 (mmmt) REVERT: H 39 ILE cc_start: 0.9089 (tp) cc_final: 0.8801 (tp) REVERT: H 51 ASP cc_start: 0.7658 (p0) cc_final: 0.7269 (p0) REVERT: H 105 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7438 (tm-30) REVERT: H 108 LYS cc_start: 0.9233 (pttt) cc_final: 0.8934 (tmmt) REVERT: R 149 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7622 (t80) REVERT: R 266 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.5888 (m-80) REVERT: N 242 MET cc_start: 0.8075 (ppp) cc_final: 0.7635 (ppp) REVERT: N 265 TYR cc_start: 0.8284 (m-10) cc_final: 0.7972 (m-10) REVERT: N 267 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8649 (m) REVERT: N 307 ARG cc_start: 0.8054 (ttp-170) cc_final: 0.7712 (ttp-170) REVERT: N 323 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7810 (mt0) REVERT: N 386 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6933 (t80) REVERT: K 5115 PHE cc_start: 0.5250 (OUTLIER) cc_final: 0.4222 (m-80) REVERT: K 5177 MET cc_start: 0.5793 (pmm) cc_final: 0.5428 (pmm) REVERT: K 5327 MET cc_start: 0.1634 (tmm) cc_final: 0.1360 (tmm) REVERT: K 5332 MET cc_start: 0.1574 (tpp) cc_final: 0.1335 (tpp) REVERT: K 5387 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: T 500 LYS cc_start: 0.5108 (ptpp) cc_final: 0.4846 (mmtt) REVERT: T 597 MET cc_start: -0.0478 (mtt) cc_final: -0.1765 (ptp) outliers start: 110 outliers final: 66 residues processed: 310 average time/residue: 0.1768 time to fit residues: 89.1872 Evaluate side-chains 279 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 205 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 LEU 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 B residue 97 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU 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 90 THR 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 57 VAL Chi-restraints excluded: chain F residue 85 ASP 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 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 116 LEU 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 38 LEU 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 143 VAL Chi-restraints excluded: chain N residue 249 VAL 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 325 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 5184 VAL Chi-restraints excluded: chain K residue 5227 CYS 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 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 T residue 409 MET Chi-restraints excluded: chain T residue 428 ASP Chi-restraints excluded: chain P residue 66 LEU 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: 0.8980 chunk 259 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 220 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 137 optimal weight: 0.0670 chunk 181 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** 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** ** G 31 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 = 0.4233 r_free = 0.4233 target = 0.110288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.074899 restraints weight = 131983.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.075015 restraints weight = 66824.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.075035 restraints weight = 53469.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.075336 restraints weight = 39459.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.075367 restraints weight = 34804.122| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2763 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= 0.163 Angle : 0.693 14.346 40576 Z= 0.368 Chirality : 0.045 0.213 4516 Planarity : 0.004 0.062 4033 Dihedral : 26.551 132.534 6487 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.24 % Favored : 93.60 % Rotamer: Outliers : 4.63 % Allowed : 21.55 % Favored : 73.82 % 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: -1.42 (0.16), residues: 2595 helix: 0.02 (0.18), residues: 769 sheet: -1.33 (0.27), residues: 359 loop : -1.37 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K5108 TYR 0.052 0.002 TYR F 88 PHE 0.021 0.001 PHE E 67 TRP 0.016 0.001 TRP K5057 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (28917) covalent geometry : angle 0.68240 / 0.37 (40546) hydrogen bonds : bond 0.04255 / 2.85 ( 1158) hydrogen bonds : angle 4.73946 / 3.38 ( 2927) metal coordination : bond 0.01073 / 0.76 ( 31) metal coordination : angle 4.57058 / 3.37 ( 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 325 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 220 time to evaluate : 0.908 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 65 LEU cc_start: 0.9681 (tp) cc_final: 0.9372 (tp) REVERT: A 73 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8839 (tm-30) REVERT: A 94 GLU cc_start: 0.8494 (tp30) cc_final: 0.8254 (tt0) REVERT: A 105 GLU cc_start: 0.8526 (pp20) cc_final: 0.8213 (tm-30) REVERT: D 93 GLU cc_start: 0.9045 (mp0) cc_final: 0.8674 (mp0) REVERT: E 41 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.6906 (t80) REVERT: E 64 LYS cc_start: 0.8861 (ptpp) cc_final: 0.8529 (ptpp) REVERT: E 120 MET cc_start: 0.8332 (mtm) cc_final: 0.8037 (mpp) REVERT: F 39 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.7913 (tpp80) REVERT: F 81 VAL cc_start: 0.9229 (OUTLIER) cc_final: 0.8914 (m) REVERT: G 36 LYS cc_start: 0.8695 (tttt) cc_final: 0.8468 (mmmt) REVERT: G 81 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8861 (tpt170) REVERT: H 39 ILE cc_start: 0.9099 (tp) cc_final: 0.8816 (tp) REVERT: H 45 LEU cc_start: 0.9430 (tp) cc_final: 0.9052 (tt) REVERT: H 51 ASP cc_start: 0.7602 (p0) cc_final: 0.7220 (p0) REVERT: H 105 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7454 (tm-30) REVERT: H 108 LYS cc_start: 0.9212 (pttt) cc_final: 0.8911 (tmmt) REVERT: R 149 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7863 (t80) REVERT: R 293 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6339 (tp) REVERT: N 242 MET cc_start: 0.7933 (ppp) cc_final: 0.7453 (ppp) REVERT: N 265 TYR cc_start: 0.8313 (m-10) cc_final: 0.8048 (m-10) REVERT: N 267 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8573 (m) REVERT: N 307 ARG cc_start: 0.8028 (ttp-170) cc_final: 0.7647 (ttp-170) REVERT: N 323 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7738 (mt0) REVERT: N 386 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6938 (t80) REVERT: K 5115 PHE cc_start: 0.5489 (OUTLIER) cc_final: 0.4350 (m-80) REVERT: K 5177 MET cc_start: 0.5906 (pmm) cc_final: 0.5496 (pmm) REVERT: K 5293 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6804 (mt) REVERT: K 5327 MET cc_start: 0.0775 (tmm) cc_final: -0.0601 (tpt) REVERT: K 5332 MET cc_start: 0.1715 (tpp) cc_final: 0.1404 (tpt) REVERT: K 5364 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.6068 (t80) REVERT: K 5387 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7681 (mp10) REVERT: K 5389 ARG cc_start: 0.8995 (ptp-170) cc_final: 0.8704 (ptp90) REVERT: T 500 LYS cc_start: 0.5111 (ptpp) cc_final: 0.4826 (mmtt) REVERT: T 597 MET cc_start: 0.0452 (mtt) cc_final: -0.1047 (ptp) REVERT: Q 76 ARG cc_start: 0.2246 (OUTLIER) cc_final: 0.1875 (tpp-160) outliers start: 105 outliers final: 60 residues processed: 304 average time/residue: 0.1922 time to fit residues: 92.4622 Evaluate side-chains 281 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 207 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 LEU 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 C residue 108 LEU 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 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 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 39 ARG 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 G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 100 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 293 ILE 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 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 325 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 1376 MET Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 1518 ASP 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 5263 VAL Chi-restraints excluded: chain K residue 5293 LEU 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 T residue 409 MET Chi-restraints excluded: chain T residue 410 VAL Chi-restraints excluded: chain T residue 428 ASP Chi-restraints excluded: chain Q residue 76 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 220 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 267 optimal weight: 9.9990 chunk 255 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.108645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.072651 restraints weight = 131571.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.073772 restraints weight = 67019.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.073642 restraints weight = 42736.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.073863 restraints weight = 38319.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.073760 restraints weight = 34651.140| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 28948 Z= 0.210 Angle : 0.717 11.659 40576 Z= 0.380 Chirality : 0.045 0.297 4516 Planarity : 0.005 0.050 4033 Dihedral : 26.709 131.892 6483 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.86 % Favored : 93.06 % Rotamer: Outliers : 4.80 % Allowed : 21.77 % Favored : 73.42 % 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: -1.37 (0.16), residues: 2595 helix: 0.08 (0.18), residues: 765 sheet: -1.30 (0.27), residues: 363 loop : -1.35 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 128 TYR 0.052 0.002 TYR F 88 PHE 0.021 0.002 PHE E 67 TRP 0.012 0.002 TRP N 51 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 (28917) covalent geometry : angle 0.70692 / 0.38 (40546) hydrogen bonds : bond 0.04970 / 3.36 ( 1158) hydrogen bonds : angle 4.72500 / 3.37 ( 2927) metal coordination : bond 0.01205 / 0.87 ( 31) metal coordination : angle 4.40034 / 3.19 ( 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 328 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 219 time to evaluate : 0.961 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 97 GLU cc_start: 0.8707 (tp30) cc_final: 0.8434 (tp30) REVERT: A 105 GLU cc_start: 0.8540 (pp20) cc_final: 0.8267 (tm-30) REVERT: B 85 ASP cc_start: 0.8349 (p0) cc_final: 0.7865 (p0) REVERT: D 93 GLU cc_start: 0.9106 (mp0) cc_final: 0.8622 (mp0) REVERT: E 41 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7001 (t80) REVERT: F 39 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.7956 (tpp80) REVERT: F 81 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.8993 (m) REVERT: G 36 LYS cc_start: 0.8881 (tttt) cc_final: 0.8608 (mmmt) REVERT: H 39 ILE cc_start: 0.9195 (tp) cc_final: 0.8893 (tp) REVERT: H 51 ASP cc_start: 0.7847 (p0) cc_final: 0.7449 (p0) REVERT: H 59 MET cc_start: 0.8629 (tpp) cc_final: 0.8151 (tpp) REVERT: H 105 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7415 (tm-30) REVERT: H 108 LYS cc_start: 0.9174 (pttt) cc_final: 0.8944 (tmmt) REVERT: R 149 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7867 (t80) REVERT: R 293 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6220 (tp) REVERT: N 242 MET cc_start: 0.7952 (ppp) cc_final: 0.7467 (ppp) REVERT: N 267 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8558 (m) REVERT: N 307 ARG cc_start: 0.8243 (ttp-170) cc_final: 0.7844 (ttp-170) REVERT: N 323 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7763 (mt0) REVERT: N 386 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6989 (t80) REVERT: K 5105 ASN cc_start: 0.5866 (OUTLIER) cc_final: 0.5170 (m110) REVERT: K 5115 PHE cc_start: 0.5540 (OUTLIER) cc_final: 0.4273 (m-80) REVERT: K 5177 MET cc_start: 0.5960 (pmm) cc_final: 0.5507 (pmm) REVERT: K 5293 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6802 (mt) REVERT: K 5332 MET cc_start: 0.1900 (tpp) cc_final: 0.1647 (tpt) REVERT: K 5364 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.5925 (t80) REVERT: K 5387 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: K 5389 ARG cc_start: 0.8953 (ptp-170) cc_final: 0.8647 (ptp90) REVERT: T 500 LYS cc_start: 0.4893 (ptpp) cc_final: 0.4668 (mmtt) REVERT: T 597 MET cc_start: -0.0031 (OUTLIER) cc_final: -0.1303 (ptp) REVERT: Q 76 ARG cc_start: 0.2099 (OUTLIER) cc_final: 0.1848 (tpp-160) outliers start: 109 outliers final: 67 residues processed: 309 average time/residue: 0.1892 time to fit residues: 94.0499 Evaluate side-chains 277 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 195 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 C residue 51 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 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 90 THR 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 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 105 GLU 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 85 ASP 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 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 ASN 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 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 38 LEU 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 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 325 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 1518 ASP 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 5105 ASN Chi-restraints excluded: chain K residue 5115 PHE Chi-restraints excluded: chain K residue 5169 ILE Chi-restraints excluded: chain K residue 5194 HIS Chi-restraints excluded: chain K residue 5227 CYS Chi-restraints excluded: chain K residue 5263 VAL Chi-restraints excluded: chain K residue 5293 LEU 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 5497 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 T residue 597 MET Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain Q residue 76 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 161 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 177 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 chunk 232 optimal weight: 5.9990 chunk 147 optimal weight: 0.0270 chunk 198 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 278 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.6640 ------------------------------------------------------------------------------- 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** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1493 ASN K1497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.109334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.070796 restraints weight = 131837.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.072311 restraints weight = 65051.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.072661 restraints weight = 43261.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.073370 restraints weight = 36450.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.073750 restraints weight = 32547.229| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28948 Z= 0.169 Angle : 0.696 13.819 40576 Z= 0.369 Chirality : 0.044 0.223 4516 Planarity : 0.004 0.049 4033 Dihedral : 26.697 132.405 6482 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 4.19 % Allowed : 23.27 % Favored : 72.54 % 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: -1.34 (0.16), residues: 2595 helix: 0.11 (0.18), residues: 767 sheet: -1.26 (0.26), residues: 375 loop : -1.33 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 99 TYR 0.057 0.002 TYR F 88 PHE 0.018 0.001 PHE E 67 TRP 0.017 0.001 TRP R 59 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (28917) covalent geometry : angle 0.68731 / 0.37 (40546) hydrogen bonds : bond 0.04151 / 2.81 ( 1158) hydrogen bonds : angle 4.58874 / 3.27 ( 2927) metal coordination : bond 0.01106 / 0.79 ( 31) metal coordination : angle 4.13059 / 3.00 ( 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 322 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 227 time to evaluate : 0.959 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 65 LEU cc_start: 0.9699 (tp) cc_final: 0.9381 (tp) REVERT: A 73 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8701 (tm-30) REVERT: A 105 GLU cc_start: 0.8570 (pp20) cc_final: 0.8307 (tm-30) REVERT: D 93 GLU cc_start: 0.9031 (mp0) cc_final: 0.8706 (mp0) REVERT: E 41 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.6947 (t80) REVERT: F 39 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.7919 (tpp80) REVERT: G 36 LYS cc_start: 0.8752 (tttt) cc_final: 0.8472 (mmmt) REVERT: G 81 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8923 (tpt170) REVERT: H 39 ILE cc_start: 0.9135 (tp) cc_final: 0.8853 (tp) REVERT: H 51 ASP cc_start: 0.7594 (p0) cc_final: 0.7171 (p0) REVERT: H 105 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7345 (tm-30) REVERT: H 108 LYS cc_start: 0.9191 (pttt) cc_final: 0.8954 (tmmt) REVERT: R 149 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7784 (t80) REVERT: N 242 MET cc_start: 0.7949 (ppp) cc_final: 0.7432 (ppp) REVERT: N 307 ARG cc_start: 0.8210 (ttp-170) cc_final: 0.7799 (ttp-170) REVERT: N 323 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7662 (mt0) REVERT: N 386 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6993 (t80) REVERT: K 5107 MET cc_start: -0.0622 (tpt) cc_final: -0.1163 (tmm) REVERT: K 5177 MET cc_start: 0.5718 (pmm) cc_final: 0.5354 (pmm) REVERT: K 5293 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6793 (mt) REVERT: K 5332 MET cc_start: 0.2085 (tpp) cc_final: 0.1836 (tpt) REVERT: K 5364 TYR cc_start: 0.6335 (OUTLIER) cc_final: 0.5783 (t80) REVERT: K 5387 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7744 (mp10) REVERT: K 5389 ARG cc_start: 0.8998 (ptp-170) cc_final: 0.8681 (ptp90) REVERT: K 5499 SER cc_start: 0.7580 (OUTLIER) cc_final: 0.6678 (p) REVERT: T 500 LYS cc_start: 0.4828 (ptpp) cc_final: 0.4563 (mmtt) REVERT: T 597 MET cc_start: -0.0431 (OUTLIER) cc_final: -0.1671 (ptp) outliers start: 95 outliers final: 61 residues processed: 300 average time/residue: 0.1792 time to fit residues: 86.7910 Evaluate side-chains 286 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 214 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 C residue 49 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU 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 90 THR 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 65 LEU 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 G residue 49 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 81 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 100 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 174 VAL Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 253 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 320 ILE Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain N residue 325 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 N residue 401 TYR Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 1478 MET Chi-restraints excluded: chain K residue 1518 ASP 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 5194 HIS Chi-restraints excluded: chain K residue 5227 CYS Chi-restraints excluded: chain K residue 5293 LEU 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 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 597 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 133 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 55 optimal weight: 0.0670 chunk 237 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- 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** G 31 HIS ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 274 HIS K1493 ASN K5051 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.109284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.073733 restraints weight = 132465.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.074839 restraints weight = 66773.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.074607 restraints weight = 43126.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.074948 restraints weight = 39178.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.074836 restraints weight = 34385.835| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3482 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= 0.160 Angle : 0.700 13.500 40576 Z= 0.370 Chirality : 0.044 0.222 4516 Planarity : 0.004 0.051 4033 Dihedral : 26.697 131.915 6482 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.36 % Favored : 93.53 % Rotamer: Outliers : 3.83 % Allowed : 24.06 % Favored : 72.10 % 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: -1.32 (0.16), residues: 2595 helix: 0.10 (0.18), residues: 766 sheet: -1.17 (0.26), residues: 370 loop : -1.33 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 99 TYR 0.061 0.002 TYR F 88 PHE 0.018 0.001 PHE E 67 TRP 0.017 0.001 TRP R 59 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (28917) covalent geometry : angle 0.69158 / 0.37 (40546) hydrogen bonds : bond 0.04102 / 2.78 ( 1158) hydrogen bonds : angle 4.49134 / 3.19 ( 2927) metal coordination : bond 0.01191 / 0.85 ( 31) metal coordination : angle 4.09604 / 2.95 ( 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: 87 poor density : 228 time to evaluate : 0.947 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 65 LEU cc_start: 0.9694 (tp) cc_final: 0.9379 (tp) REVERT: A 73 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8605 (tm-30) REVERT: A 105 GLU cc_start: 0.8573 (pp20) cc_final: 0.8293 (tm-30) REVERT: D 93 GLU cc_start: 0.9005 (mp0) cc_final: 0.8703 (mp0) REVERT: E 41 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.6955 (t80) REVERT: F 39 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.7902 (tpp80) REVERT: F 81 VAL cc_start: 0.9292 (OUTLIER) cc_final: 0.9041 (m) REVERT: G 36 LYS cc_start: 0.8745 (tttt) cc_final: 0.8461 (mmmt) REVERT: G 81 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8912 (tpt170) REVERT: H 39 ILE cc_start: 0.9110 (tp) cc_final: 0.8822 (tp) REVERT: H 51 ASP cc_start: 0.7749 (p0) cc_final: 0.7328 (p0) REVERT: H 59 MET cc_start: 0.8513 (tpp) cc_final: 0.7870 (tpp) REVERT: H 108 LYS cc_start: 0.9167 (pttt) cc_final: 0.8964 (tmmt) REVERT: R 149 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7942 (t80) REVERT: R 243 TYR cc_start: 0.7351 (p90) cc_final: 0.6626 (p90) REVERT: N 242 MET cc_start: 0.7920 (ppp) cc_final: 0.7405 (ppp) REVERT: N 267 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8591 (m) REVERT: N 307 ARG cc_start: 0.8227 (ttp-170) cc_final: 0.7806 (ttp-170) REVERT: N 323 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: N 386 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6982 (t80) REVERT: K 5177 MET cc_start: 0.5811 (pmm) cc_final: 0.5391 (pmm) REVERT: K 5293 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6816 (mt) REVERT: K 5332 MET cc_start: 0.2235 (tpp) cc_final: 0.1973 (tpp) REVERT: K 5364 TYR cc_start: 0.6402 (OUTLIER) cc_final: 0.5603 (t80) REVERT: K 5387 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7721 (mp10) REVERT: K 5389 ARG cc_start: 0.8974 (ptp-170) cc_final: 0.8663 (ptp90) REVERT: K 5452 MET cc_start: 0.8055 (mpp) cc_final: 0.7200 (mtm) REVERT: K 5499 SER cc_start: 0.7401 (OUTLIER) cc_final: 0.6546 (p) REVERT: T 500 LYS cc_start: 0.4895 (ptpp) cc_final: 0.4603 (mmtt) outliers start: 87 outliers final: 64 residues processed: 296 average time/residue: 0.1848 time to fit residues: 87.7966 Evaluate side-chains 292 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 216 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 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 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 114 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 90 THR 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 65 LEU 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 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 81 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 100 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 174 VAL Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 253 THR 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 214 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 325 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 N residue 401 TYR Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 1478 MET 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 5194 HIS Chi-restraints excluded: chain K residue 5227 CYS Chi-restraints excluded: chain K residue 5293 LEU 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 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 459 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 91 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 251 optimal weight: 0.2980 chunk 197 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5356 ASN ** 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 = 0.4214 r_free = 0.4214 target = 0.108901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.073202 restraints weight = 133347.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.073753 restraints weight = 66844.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.073652 restraints weight = 47353.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.074214 restraints weight = 37942.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.074006 restraints weight = 32085.622| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28948 Z= 0.169 Angle : 0.705 13.280 40576 Z= 0.373 Chirality : 0.044 0.309 4516 Planarity : 0.004 0.052 4033 Dihedral : 26.721 131.809 6482 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.67 % Favored : 93.22 % Rotamer: Outliers : 3.79 % Allowed : 24.15 % Favored : 72.06 % 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: -1.33 (0.16), residues: 2595 helix: 0.10 (0.18), residues: 763 sheet: -1.20 (0.26), residues: 381 loop : -1.33 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 33 TYR 0.059 0.002 TYR F 88 PHE 0.018 0.001 PHE N 332 TRP 0.017 0.002 TRP R 59 HIS 0.011 0.001 HIS K1531 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (28917) covalent geometry : angle 0.69639 / 0.37 (40546) hydrogen bonds : bond 0.04156 / 2.82 ( 1158) hydrogen bonds : angle 4.43461 / 3.15 ( 2927) metal coordination : bond 0.00913 / 0.65 ( 31) metal coordination : angle 4.14192 / 2.95 ( 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 308 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 222 time to evaluate : 0.931 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 65 LEU cc_start: 0.9696 (tp) cc_final: 0.9378 (tp) REVERT: A 73 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8665 (tm-30) REVERT: A 105 GLU cc_start: 0.8587 (pp20) cc_final: 0.8285 (tm-30) REVERT: B 44 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8427 (mttt) REVERT: D 93 GLU cc_start: 0.9022 (mp0) cc_final: 0.8698 (mp0) REVERT: E 41 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.6922 (t80) REVERT: F 39 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7905 (tpp80) REVERT: F 81 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9085 (m) REVERT: G 36 LYS cc_start: 0.8789 (tttt) cc_final: 0.8507 (mmmt) REVERT: G 81 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8920 (tpt170) REVERT: H 39 ILE cc_start: 0.9167 (tp) cc_final: 0.8901 (tp) REVERT: H 105 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7534 (tm-30) REVERT: R 149 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7858 (t80) REVERT: R 243 TYR cc_start: 0.7390 (p90) cc_final: 0.6638 (p90) REVERT: N 242 MET cc_start: 0.7926 (ppp) cc_final: 0.7427 (ppp) REVERT: N 267 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8466 (m) REVERT: N 307 ARG cc_start: 0.8290 (ttp-170) cc_final: 0.8004 (ttp-170) REVERT: N 323 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: N 386 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.7055 (t80) REVERT: K 5107 MET cc_start: 0.0425 (tmm) cc_final: -0.0061 (tpt) REVERT: K 5115 PHE cc_start: 0.5639 (OUTLIER) cc_final: 0.4225 (m-80) REVERT: K 5177 MET cc_start: 0.5838 (pmm) cc_final: 0.5422 (pmm) REVERT: K 5293 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6858 (mp) REVERT: K 5327 MET cc_start: -0.0111 (tmm) cc_final: -0.1498 (tpt) REVERT: K 5332 MET cc_start: 0.2423 (tpp) cc_final: 0.2164 (tpp) REVERT: K 5364 TYR cc_start: 0.6419 (OUTLIER) cc_final: 0.5512 (t80) REVERT: K 5389 ARG cc_start: 0.8988 (ptp-170) cc_final: 0.8683 (ptp90) REVERT: K 5499 SER cc_start: 0.7433 (OUTLIER) cc_final: 0.6598 (p) REVERT: T 500 LYS cc_start: 0.4857 (ptpp) cc_final: 0.4558 (mmtt) outliers start: 86 outliers final: 65 residues processed: 288 average time/residue: 0.1869 time to fit residues: 86.6125 Evaluate side-chains 292 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 215 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 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 90 THR 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 65 LEU 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 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 81 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 100 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 174 VAL Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 253 THR 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 214 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 325 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 N residue 401 TYR Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 1478 MET 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 5194 HIS Chi-restraints excluded: chain K residue 5227 CYS Chi-restraints excluded: chain K residue 5263 VAL Chi-restraints excluded: chain K residue 5293 LEU 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 5455 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 459 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 284 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 124 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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** H 109 HIS ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1531 HIS K5061 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.108298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.072466 restraints weight = 132661.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.073699 restraints weight = 67579.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.074150 restraints weight = 41692.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.073825 restraints weight = 37762.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.073835 restraints weight = 33569.579| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28948 Z= 0.181 Angle : 0.718 14.393 40576 Z= 0.378 Chirality : 0.045 0.229 4516 Planarity : 0.004 0.064 4033 Dihedral : 26.817 132.156 6481 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.67 % Favored : 93.22 % Rotamer: Outliers : 3.57 % Allowed : 24.55 % Favored : 71.88 % 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: -1.34 (0.16), residues: 2595 helix: 0.07 (0.19), residues: 763 sheet: -1.22 (0.25), residues: 381 loop : -1.32 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 33 TYR 0.065 0.002 TYR F 88 PHE 0.017 0.001 PHE E 67 TRP 0.019 0.002 TRP R 59 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (28917) covalent geometry : angle 0.70847 / 0.38 (40546) hydrogen bonds : bond 0.04359 / 2.94 ( 1158) hydrogen bonds : angle 4.44248 / 3.16 ( 2927) metal coordination : bond 0.01064 / 0.75 ( 31) metal coordination : angle 4.35507 / 3.13 ( 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 301 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 220 time to evaluate : 0.899 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 65 LEU cc_start: 0.9705 (tp) cc_final: 0.9392 (tp) REVERT: A 73 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8786 (tm-30) REVERT: A 105 GLU cc_start: 0.8618 (pp20) cc_final: 0.8310 (tm-30) REVERT: D 89 ILE cc_start: 0.8923 (mt) cc_final: 0.8661 (mp) REVERT: D 93 GLU cc_start: 0.9051 (mp0) cc_final: 0.8687 (mp0) REVERT: E 41 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.6953 (t80) REVERT: F 39 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.7934 (tpp80) REVERT: G 36 LYS cc_start: 0.8845 (tttt) cc_final: 0.8546 (mmmt) REVERT: G 81 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8763 (tpt170) REVERT: H 39 ILE cc_start: 0.9211 (tp) cc_final: 0.8958 (tp) REVERT: H 43 LYS cc_start: 0.9378 (mptt) cc_final: 0.8968 (ttmm) REVERT: H 59 MET cc_start: 0.8425 (tpp) cc_final: 0.8148 (tpp) REVERT: R 243 TYR cc_start: 0.7394 (p90) cc_final: 0.6606 (p90) REVERT: N 242 MET cc_start: 0.7930 (ppp) cc_final: 0.7424 (ppp) REVERT: N 265 TYR cc_start: 0.8378 (m-10) cc_final: 0.7913 (m-10) REVERT: N 267 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8425 (m) REVERT: N 323 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7640 (mt0) REVERT: N 386 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.7121 (t80) REVERT: K 5107 MET cc_start: 0.0326 (tmm) cc_final: 0.0034 (tpt) REVERT: K 5115 PHE cc_start: 0.5689 (OUTLIER) cc_final: 0.4308 (m-80) REVERT: K 5177 MET cc_start: 0.5843 (pmm) cc_final: 0.5429 (pmm) REVERT: K 5293 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6750 (mp) REVERT: K 5327 MET cc_start: 0.0021 (tmm) cc_final: -0.1470 (tpt) REVERT: K 5364 TYR cc_start: 0.6512 (OUTLIER) cc_final: 0.5802 (t80) REVERT: K 5389 ARG cc_start: 0.8963 (ptp-170) cc_final: 0.8660 (ptp90) REVERT: K 5452 MET cc_start: 0.8088 (mpp) cc_final: 0.7185 (mtm) REVERT: K 5499 SER cc_start: 0.7382 (OUTLIER) cc_final: 0.6586 (p) REVERT: K 5536 MET cc_start: 0.5772 (mmt) cc_final: 0.5504 (mmm) REVERT: T 500 LYS cc_start: 0.4938 (ptpp) cc_final: 0.4651 (mmtt) outliers start: 81 outliers final: 65 residues processed: 279 average time/residue: 0.1918 time to fit residues: 85.3639 Evaluate side-chains 287 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 212 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 58 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 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 90 THR 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 65 LEU 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 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 81 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 100 LEU 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 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 125 VAL Chi-restraints excluded: chain N residue 214 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 325 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 N residue 401 TYR Chi-restraints excluded: chain K residue 1410 ASN Chi-restraints excluded: chain K residue 1478 MET 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 5194 HIS Chi-restraints excluded: chain K residue 5227 CYS Chi-restraints excluded: chain K residue 5293 LEU 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 5455 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 459 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 127 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 283 optimal weight: 9.9990 chunk 200 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** 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 = 0.4206 r_free = 0.4206 target = 0.108381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.072073 restraints weight = 132308.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.073009 restraints weight = 66089.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.072687 restraints weight = 47116.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.073247 restraints weight = 40074.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.073141 restraints weight = 33084.909| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28948 Z= 0.173 Angle : 0.711 14.188 40576 Z= 0.375 Chirality : 0.044 0.231 4516 Planarity : 0.004 0.052 4033 Dihedral : 26.831 132.475 6481 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.47 % Favored : 93.41 % Rotamer: Outliers : 3.44 % Allowed : 24.81 % Favored : 71.75 % 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: -1.29 (0.16), residues: 2595 helix: 0.10 (0.19), residues: 769 sheet: -1.14 (0.25), residues: 382 loop : -1.29 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 116 TYR 0.066 0.002 TYR F 88 PHE 0.016 0.001 PHE E 67 TRP 0.019 0.002 TRP R 59 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (28917) covalent geometry : angle 0.70158 / 0.37 (40546) hydrogen bonds : bond 0.04141 / 2.81 ( 1158) hydrogen bonds : angle 4.41392 / 3.13 ( 2927) metal coordination : bond 0.01058 / 0.74 ( 31) metal coordination : angle 4.20740 / 3.03 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6557.82 seconds wall clock time: 113 minutes 33.69 seconds (6813.69 seconds total)