Starting phenix.real_space_refine on Mon Nov 18 18:58:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vbx_43127/11_2024/8vbx_43127.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vbx_43127/11_2024/8vbx_43127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vbx_43127/11_2024/8vbx_43127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vbx_43127/11_2024/8vbx_43127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vbx_43127/11_2024/8vbx_43127.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vbx_43127/11_2024/8vbx_43127.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.064 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: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 31656 2.51 5 N 8466 2.21 5 O 9774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 366 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 50010 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 4875 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 31, 'TRANS': 617} Chain breaks: 2 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 12, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 112 Chain: "M" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 146} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1174 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: O, N, Q, P, R, C, B, E, D, F, U, T, W, V, X, I, H, K, J, L Time building chain proxies: 17.54, per 1000 atoms: 0.35 Number of scatterers: 50010 At special positions: 0 Unit cell: (239.4, 245, 168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 9774 8.00 N 8466 7.00 C 31656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.67 Conformation dependent library (CDL) restraints added in 6.2 seconds 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12048 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 126 sheets defined 11.8% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.46 Creating SS restraints... Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.676A pdb=" N VAL A 106 " --> pdb=" O GLN A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.759A pdb=" N ASN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'R' and resid 24 through 26 No H-bonds generated for 'chain 'R' and resid 24 through 26' Processing helix chain 'R' and resid 81 through 85 removed outlier: 3.616A pdb=" N GLY R 85 " --> pdb=" O TYR R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 109 removed outlier: 3.762A pdb=" N LEU R 93 " --> pdb=" O ASN R 89 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU R 109 " --> pdb=" O GLN R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 146 Processing helix chain 'Q' and resid 24 through 26 No H-bonds generated for 'chain 'Q' and resid 24 through 26' Processing helix chain 'Q' and resid 81 through 85 removed outlier: 3.616A pdb=" N GLY Q 85 " --> pdb=" O TYR Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 109 removed outlier: 3.763A pdb=" N LEU Q 93 " --> pdb=" O ASN Q 89 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU Q 109 " --> pdb=" O GLN Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 146 Processing helix chain 'P' and resid 24 through 26 No H-bonds generated for 'chain 'P' and resid 24 through 26' Processing helix chain 'P' and resid 81 through 85 removed outlier: 3.615A pdb=" N GLY P 85 " --> pdb=" O TYR P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 109 removed outlier: 3.762A pdb=" N LEU P 93 " --> pdb=" O ASN P 89 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU P 109 " --> pdb=" O GLN P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 Processing helix chain 'O' and resid 24 through 26 No H-bonds generated for 'chain 'O' and resid 24 through 26' Processing helix chain 'O' and resid 81 through 85 removed outlier: 3.616A pdb=" N GLY O 85 " --> pdb=" O TYR O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 109 removed outlier: 3.762A pdb=" N LEU O 93 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU O 109 " --> pdb=" O GLN O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 146 Processing helix chain 'N' and resid 24 through 26 No H-bonds generated for 'chain 'N' and resid 24 through 26' Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.615A pdb=" N GLY N 85 " --> pdb=" O TYR N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 109 removed outlier: 3.762A pdb=" N LEU N 93 " --> pdb=" O ASN N 89 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU N 109 " --> pdb=" O GLN N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 146 Processing helix chain 'M' and resid 24 through 26 No H-bonds generated for 'chain 'M' and resid 24 through 26' Processing helix chain 'M' and resid 81 through 85 removed outlier: 3.615A pdb=" N GLY M 85 " --> pdb=" O TYR M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 109 removed outlier: 3.762A pdb=" N LEU M 93 " --> pdb=" O ASN M 89 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU M 109 " --> pdb=" O GLN M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 146 Processing helix chain 'X' and resid 24 through 28 removed outlier: 3.500A pdb=" N ILE X 28 " --> pdb=" O LYS X 25 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 85 Processing helix chain 'X' and resid 90 through 109 removed outlier: 3.668A pdb=" N ASN X 96 " --> pdb=" O THR X 92 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU X 109 " --> pdb=" O GLN X 105 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 151 Processing helix chain 'W' and resid 24 through 28 removed outlier: 3.500A pdb=" N ILE W 28 " --> pdb=" O LYS W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 81 through 85 Processing helix chain 'W' and resid 90 through 109 removed outlier: 3.667A pdb=" N ASN W 96 " --> pdb=" O THR W 92 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU W 109 " --> pdb=" O GLN W 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 144 through 151 Processing helix chain 'V' and resid 24 through 28 Processing helix chain 'V' and resid 81 through 85 Processing helix chain 'V' and resid 90 through 109 removed outlier: 3.668A pdb=" N ASN V 96 " --> pdb=" O THR V 92 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU V 109 " --> pdb=" O GLN V 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 144 through 151 Processing helix chain 'U' and resid 24 through 28 removed outlier: 3.500A pdb=" N ILE U 28 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 85 Processing helix chain 'U' and resid 90 through 109 removed outlier: 3.668A pdb=" N ASN U 96 " --> pdb=" O THR U 92 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU U 109 " --> pdb=" O GLN U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 144 through 151 Processing helix chain 'T' and resid 24 through 28 removed outlier: 3.500A pdb=" N ILE T 28 " --> pdb=" O LYS T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 85 Processing helix chain 'T' and resid 90 through 109 removed outlier: 3.667A pdb=" N ASN T 96 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU T 109 " --> pdb=" O GLN T 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 144 through 151 Processing helix chain 'S' and resid 24 through 28 Processing helix chain 'S' and resid 81 through 85 Processing helix chain 'S' and resid 90 through 109 removed outlier: 3.668A pdb=" N ASN S 96 " --> pdb=" O THR S 92 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU S 109 " --> pdb=" O GLN S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 151 Processing helix chain 'L' and resid 24 through 26 No H-bonds generated for 'chain 'L' and resid 24 through 26' Processing helix chain 'L' and resid 90 through 109 removed outlier: 3.834A pdb=" N ASN L 96 " --> pdb=" O THR L 92 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET L 100 " --> pdb=" O ASN L 96 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE L 101 " --> pdb=" O PHE L 97 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU L 109 " --> pdb=" O GLN L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 152 removed outlier: 3.953A pdb=" N THR L 150 " --> pdb=" O ASP L 146 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA L 151 " --> pdb=" O THR L 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 26 No H-bonds generated for 'chain 'K' and resid 24 through 26' Processing helix chain 'K' and resid 90 through 109 removed outlier: 3.835A pdb=" N ASN K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET K 100 " --> pdb=" O ASN K 96 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE K 101 " --> pdb=" O PHE K 97 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU K 109 " --> pdb=" O GLN K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 152 removed outlier: 3.954A pdb=" N THR K 150 " --> pdb=" O ASP K 146 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA K 151 " --> pdb=" O THR K 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 26 No H-bonds generated for 'chain 'J' and resid 24 through 26' Processing helix chain 'J' and resid 90 through 109 removed outlier: 3.835A pdb=" N ASN J 96 " --> pdb=" O THR J 92 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET J 100 " --> pdb=" O ASN J 96 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE J 101 " --> pdb=" O PHE J 97 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU J 109 " --> pdb=" O GLN J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 152 removed outlier: 3.954A pdb=" N THR J 150 " --> pdb=" O ASP J 146 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA J 151 " --> pdb=" O THR J 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 26 No H-bonds generated for 'chain 'I' and resid 24 through 26' Processing helix chain 'I' and resid 90 through 109 removed outlier: 3.835A pdb=" N ASN I 96 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET I 100 " --> pdb=" O ASN I 96 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE I 101 " --> pdb=" O PHE I 97 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU I 109 " --> pdb=" O GLN I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 152 removed outlier: 3.953A pdb=" N THR I 150 " --> pdb=" O ASP I 146 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA I 151 " --> pdb=" O THR I 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 26 No H-bonds generated for 'chain 'H' and resid 24 through 26' Processing helix chain 'H' and resid 90 through 109 removed outlier: 3.835A pdb=" N ASN H 96 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET H 100 " --> pdb=" O ASN H 96 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE H 101 " --> pdb=" O PHE H 97 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU H 109 " --> pdb=" O GLN H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 152 removed outlier: 3.954A pdb=" N THR H 150 " --> pdb=" O ASP H 146 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA H 151 " --> pdb=" O THR H 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 26 No H-bonds generated for 'chain 'G' and resid 24 through 26' Processing helix chain 'G' and resid 90 through 109 removed outlier: 3.835A pdb=" N ASN G 96 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET G 100 " --> pdb=" O ASN G 96 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE G 101 " --> pdb=" O PHE G 97 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU G 109 " --> pdb=" O GLN G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 removed outlier: 3.954A pdb=" N THR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA G 151 " --> pdb=" O THR G 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 removed outlier: 3.674A pdb=" N VAL B 106 " --> pdb=" O GLN B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.759A pdb=" N ASN B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 603 No H-bonds generated for 'chain 'B' and resid 601 through 603' Processing helix chain 'B' and resid 604 through 609 Processing helix chain 'C' and resid 103 through 106 removed outlier: 3.676A pdb=" N VAL C 106 " --> pdb=" O GLN C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.760A pdb=" N ASN C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 603 No H-bonds generated for 'chain 'C' and resid 601 through 603' Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.676A pdb=" N VAL D 106 " --> pdb=" O GLN D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.760A pdb=" N ASN D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 603 No H-bonds generated for 'chain 'D' and resid 601 through 603' Processing helix chain 'D' and resid 604 through 609 Processing helix chain 'E' and resid 103 through 106 removed outlier: 3.675A pdb=" N VAL E 106 " --> pdb=" O GLN E 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 106' Processing helix chain 'E' and resid 335 through 340 removed outlier: 3.759A pdb=" N ASN E 339 " --> pdb=" O GLY E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 603 No H-bonds generated for 'chain 'E' and resid 601 through 603' Processing helix chain 'E' and resid 604 through 609 Processing helix chain 'F' and resid 103 through 106 removed outlier: 3.676A pdb=" N VAL F 106 " --> pdb=" O GLN F 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 103 through 106' Processing helix chain 'F' and resid 335 through 340 removed outlier: 3.760A pdb=" N ASN F 339 " --> pdb=" O GLY F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 601 through 603 No H-bonds generated for 'chain 'F' and resid 601 through 603' Processing helix chain 'F' and resid 604 through 609 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.692A pdb=" N ASP A 762 " --> pdb=" O THR A 689 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A 685 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN A 768 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU A 683 " --> pdb=" O GLN A 768 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ARG A 685 " --> pdb=" O VAL A 739 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 739 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLU A 687 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE A 737 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N THR A 689 " --> pdb=" O THR A 735 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR A 735 " --> pdb=" O THR A 689 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 30 removed outlier: 3.597A pdb=" N VAL A 29 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 56 removed outlier: 7.103A pdb=" N VAL A 566 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP A 52 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 564 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET A 558 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR A 555 " --> pdb=" O THR A 547 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR A 547 " --> pdb=" O TYR A 555 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY A 557 " --> pdb=" O VAL A 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 70 removed outlier: 3.617A pdb=" N HIS A 98 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 113 through 117 removed outlier: 3.562A pdb=" N ARG A 306 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 132 through 134 removed outlier: 3.518A pdb=" N VAL A 134 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 299 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA8, first strand: chain 'A' and resid 345 through 347 Processing sheet with id=AA9, first strand: chain 'A' and resid 398 through 400 removed outlier: 4.123A pdb=" N HIS A 398 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 406 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN A 414 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 446 through 447 removed outlier: 6.643A pdb=" N PHE A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 495 through 501 removed outlier: 6.376A pdb=" N ILE A 510 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A 498 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 508 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER A 500 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N SER A 506 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N CYS A 511 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER A 517 " --> pdb=" O CYS A 511 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU A 518 " --> pdb=" O GLN A 537 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN A 537 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE A 520 " --> pdb=" O TRP A 535 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TRP A 535 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ASP A 522 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 533 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 524 " --> pdb=" O VAL A 531 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 586 through 593 removed outlier: 6.229A pdb=" N VAL A 587 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU A 655 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 649 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 616 " --> pdb=" O VAL A 628 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 597 through 599 removed outlier: 6.162A pdb=" N VAL A 639 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE A 633 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR A 641 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 706 through 712 removed outlier: 3.625A pdb=" N GLY A 710 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 698 " --> pdb=" O GLY A 710 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 4 through 8 Processing sheet with id=AB7, first strand: chain 'R' and resid 15 through 17 Processing sheet with id=AB8, first strand: chain 'R' and resid 127 through 128 Processing sheet with id=AB9, first strand: chain 'Q' and resid 4 through 8 Processing sheet with id=AC1, first strand: chain 'Q' and resid 15 through 17 Processing sheet with id=AC2, first strand: chain 'Q' and resid 127 through 128 Processing sheet with id=AC3, first strand: chain 'P' and resid 4 through 8 Processing sheet with id=AC4, first strand: chain 'P' and resid 15 through 17 Processing sheet with id=AC5, first strand: chain 'P' and resid 127 through 128 Processing sheet with id=AC6, first strand: chain 'O' and resid 4 through 8 Processing sheet with id=AC7, first strand: chain 'O' and resid 15 through 17 Processing sheet with id=AC8, first strand: chain 'O' and resid 127 through 128 Processing sheet with id=AC9, first strand: chain 'N' and resid 4 through 8 Processing sheet with id=AD1, first strand: chain 'N' and resid 15 through 17 Processing sheet with id=AD2, first strand: chain 'N' and resid 127 through 128 Processing sheet with id=AD3, first strand: chain 'M' and resid 4 through 8 Processing sheet with id=AD4, first strand: chain 'M' and resid 15 through 17 Processing sheet with id=AD5, first strand: chain 'M' and resid 127 through 128 Processing sheet with id=AD6, first strand: chain 'X' and resid 5 through 8 Processing sheet with id=AD7, first strand: chain 'X' and resid 15 through 17 Processing sheet with id=AD8, first strand: chain 'W' and resid 5 through 8 Processing sheet with id=AD9, first strand: chain 'W' and resid 15 through 17 Processing sheet with id=AE1, first strand: chain 'V' and resid 5 through 8 Processing sheet with id=AE2, first strand: chain 'V' and resid 15 through 17 Processing sheet with id=AE3, first strand: chain 'U' and resid 5 through 8 Processing sheet with id=AE4, first strand: chain 'U' and resid 15 through 17 Processing sheet with id=AE5, first strand: chain 'T' and resid 5 through 8 Processing sheet with id=AE6, first strand: chain 'T' and resid 15 through 17 Processing sheet with id=AE7, first strand: chain 'S' and resid 5 through 8 Processing sheet with id=AE8, first strand: chain 'S' and resid 15 through 17 Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 8 removed outlier: 3.640A pdb=" N THR L 68 " --> pdb=" O TYR L 31 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR L 31 " --> pdb=" O THR L 68 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 15 through 17 Processing sheet with id=AF2, first strand: chain 'K' and resid 4 through 8 removed outlier: 3.641A pdb=" N THR K 68 " --> pdb=" O TYR K 31 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR K 31 " --> pdb=" O THR K 68 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 15 through 17 Processing sheet with id=AF4, first strand: chain 'J' and resid 4 through 8 removed outlier: 3.641A pdb=" N THR J 68 " --> pdb=" O TYR J 31 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR J 31 " --> pdb=" O THR J 68 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 15 through 17 Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 8 removed outlier: 3.640A pdb=" N THR I 68 " --> pdb=" O TYR I 31 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR I 31 " --> pdb=" O THR I 68 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 15 through 17 Processing sheet with id=AF8, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.641A pdb=" N THR H 68 " --> pdb=" O TYR H 31 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR H 31 " --> pdb=" O THR H 68 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 15 through 17 Processing sheet with id=AG1, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.641A pdb=" N THR G 68 " --> pdb=" O TYR G 31 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR G 31 " --> pdb=" O THR G 68 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=AG3, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.692A pdb=" N ASP B 762 " --> pdb=" O THR B 689 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 685 " --> pdb=" O VAL B 766 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN B 768 " --> pdb=" O LEU B 683 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU B 683 " --> pdb=" O GLN B 768 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ARG B 685 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 739 " --> pdb=" O ARG B 685 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLU B 687 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE B 737 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N THR B 689 " --> pdb=" O THR B 735 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR B 735 " --> pdb=" O THR B 689 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.596A pdb=" N VAL B 29 " --> pdb=" O SER B 662 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 48 through 56 removed outlier: 7.103A pdb=" N VAL B 566 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP B 52 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE B 564 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET B 558 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR B 555 " --> pdb=" O THR B 547 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR B 547 " --> pdb=" O TYR B 555 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY B 557 " --> pdb=" O VAL B 545 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 63 through 70 removed outlier: 3.617A pdb=" N HIS B 98 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 113 through 117 removed outlier: 3.563A pdb=" N ARG B 306 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 132 through 134 removed outlier: 3.517A pdb=" N VAL B 134 " --> pdb=" O GLY B 299 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 299 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 267 through 269 Processing sheet with id=AH1, first strand: chain 'B' and resid 345 through 347 Processing sheet with id=AH2, first strand: chain 'B' and resid 398 through 400 removed outlier: 4.124A pdb=" N HIS B 398 " --> pdb=" O PHE B 409 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 406 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN B 414 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 446 through 447 removed outlier: 6.644A pdb=" N PHE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 495 through 501 removed outlier: 6.376A pdb=" N ILE B 510 " --> pdb=" O ARG B 496 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE B 498 " --> pdb=" O ALA B 508 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA B 508 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER B 500 " --> pdb=" O SER B 506 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N SER B 506 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N CYS B 511 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER B 517 " --> pdb=" O CYS B 511 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 518 " --> pdb=" O GLN B 537 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN B 537 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE B 520 " --> pdb=" O TRP B 535 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TRP B 535 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ASP B 522 " --> pdb=" O SER B 533 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 533 " --> pdb=" O ASP B 522 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 524 " --> pdb=" O VAL B 531 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 586 through 593 removed outlier: 6.229A pdb=" N VAL B 587 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU B 655 " --> pdb=" O VAL B 587 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 649 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE B 616 " --> pdb=" O VAL B 628 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 597 through 599 removed outlier: 6.162A pdb=" N VAL B 639 " --> pdb=" O ILE B 633 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 633 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR B 641 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 706 through 712 removed outlier: 3.624A pdb=" N GLY B 710 " --> pdb=" O ALA B 698 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 698 " --> pdb=" O GLY B 710 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.692A pdb=" N ASP C 762 " --> pdb=" O THR C 689 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG C 685 " --> pdb=" O VAL C 766 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN C 768 " --> pdb=" O LEU C 683 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU C 683 " --> pdb=" O GLN C 768 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ARG C 685 " --> pdb=" O VAL C 739 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL C 739 " --> pdb=" O ARG C 685 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLU C 687 " --> pdb=" O ILE C 737 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE C 737 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N THR C 689 " --> pdb=" O THR C 735 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR C 735 " --> pdb=" O THR C 689 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.597A pdb=" N VAL C 29 " --> pdb=" O SER C 662 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 48 through 56 removed outlier: 7.102A pdb=" N VAL C 566 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP C 52 " --> pdb=" O ILE C 564 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE C 564 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET C 558 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR C 555 " --> pdb=" O THR C 547 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR C 547 " --> pdb=" O TYR C 555 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY C 557 " --> pdb=" O VAL C 545 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 63 through 70 removed outlier: 3.617A pdb=" N HIS C 98 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 113 through 117 removed outlier: 3.561A pdb=" N ARG C 306 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 132 through 134 removed outlier: 3.518A pdb=" N VAL C 134 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 299 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 267 through 269 Processing sheet with id=AI6, first strand: chain 'C' and resid 345 through 347 Processing sheet with id=AI7, first strand: chain 'C' and resid 398 through 400 removed outlier: 4.125A pdb=" N HIS C 398 " --> pdb=" O PHE C 409 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 406 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLN C 414 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'C' and resid 446 through 447 removed outlier: 6.644A pdb=" N PHE C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'C' and resid 495 through 501 removed outlier: 6.376A pdb=" N ILE C 510 " --> pdb=" O ARG C 496 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE C 498 " --> pdb=" O ALA C 508 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA C 508 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER C 500 " --> pdb=" O SER C 506 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER C 506 " --> pdb=" O SER C 500 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N CYS C 511 " --> pdb=" O SER C 517 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER C 517 " --> pdb=" O CYS C 511 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 518 " --> pdb=" O GLN C 537 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN C 537 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE C 520 " --> pdb=" O TRP C 535 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TRP C 535 " --> pdb=" O ILE C 520 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ASP C 522 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 533 " --> pdb=" O ASP C 522 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU C 524 " --> pdb=" O VAL C 531 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'C' and resid 586 through 593 removed outlier: 6.229A pdb=" N VAL C 587 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU C 655 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY C 649 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE C 616 " --> pdb=" O VAL C 628 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'C' and resid 597 through 599 removed outlier: 6.161A pdb=" N VAL C 639 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE C 633 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR C 641 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'C' and resid 706 through 712 removed outlier: 3.625A pdb=" N GLY C 710 " --> pdb=" O ALA C 698 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 698 " --> pdb=" O GLY C 710 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.692A pdb=" N ASP D 762 " --> pdb=" O THR D 689 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG D 685 " --> pdb=" O VAL D 766 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN D 768 " --> pdb=" O LEU D 683 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU D 683 " --> pdb=" O GLN D 768 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ARG D 685 " --> pdb=" O VAL D 739 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL D 739 " --> pdb=" O ARG D 685 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLU D 687 " --> pdb=" O ILE D 737 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE D 737 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N THR D 689 " --> pdb=" O THR D 735 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR D 735 " --> pdb=" O THR D 689 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'D' and resid 29 through 30 removed outlier: 3.597A pdb=" N VAL D 29 " --> pdb=" O SER D 662 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'D' and resid 48 through 56 removed outlier: 7.103A pdb=" N VAL D 566 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP D 52 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE D 564 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET D 558 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR D 555 " --> pdb=" O THR D 547 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR D 547 " --> pdb=" O TYR D 555 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY D 557 " --> pdb=" O VAL D 545 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'D' and resid 63 through 70 removed outlier: 3.617A pdb=" N HIS D 98 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'D' and resid 113 through 117 removed outlier: 3.562A pdb=" N ARG D 306 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'D' and resid 132 through 134 removed outlier: 3.516A pdb=" N VAL D 134 " --> pdb=" O GLY D 299 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY D 299 " --> pdb=" O VAL D 134 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'D' and resid 267 through 269 Processing sheet with id=AK2, first strand: chain 'D' and resid 345 through 347 Processing sheet with id=AK3, first strand: chain 'D' and resid 398 through 400 removed outlier: 4.124A pdb=" N HIS D 398 " --> pdb=" O PHE D 409 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 406 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLN D 414 " --> pdb=" O THR D 434 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'D' and resid 446 through 447 removed outlier: 6.644A pdb=" N PHE D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'D' and resid 495 through 501 removed outlier: 6.376A pdb=" N ILE D 510 " --> pdb=" O ARG D 496 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE D 498 " --> pdb=" O ALA D 508 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA D 508 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER D 500 " --> pdb=" O SER D 506 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N SER D 506 " --> pdb=" O SER D 500 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N CYS D 511 " --> pdb=" O SER D 517 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER D 517 " --> pdb=" O CYS D 511 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU D 518 " --> pdb=" O GLN D 537 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN D 537 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE D 520 " --> pdb=" O TRP D 535 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TRP D 535 " --> pdb=" O ILE D 520 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ASP D 522 " --> pdb=" O SER D 533 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 533 " --> pdb=" O ASP D 522 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU D 524 " --> pdb=" O VAL D 531 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'D' and resid 586 through 593 removed outlier: 6.229A pdb=" N VAL D 587 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU D 655 " --> pdb=" O VAL D 587 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY D 649 " --> pdb=" O ILE D 593 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE D 616 " --> pdb=" O VAL D 628 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'D' and resid 597 through 599 removed outlier: 6.161A pdb=" N VAL D 639 " --> pdb=" O ILE D 633 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE D 633 " --> pdb=" O VAL D 639 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR D 641 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'D' and resid 706 through 712 removed outlier: 3.624A pdb=" N GLY D 710 " --> pdb=" O ALA D 698 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 698 " --> pdb=" O GLY D 710 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.692A pdb=" N ASP E 762 " --> pdb=" O THR E 689 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG E 685 " --> pdb=" O VAL E 766 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN E 768 " --> pdb=" O LEU E 683 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU E 683 " --> pdb=" O GLN E 768 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ARG E 685 " --> pdb=" O VAL E 739 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL E 739 " --> pdb=" O ARG E 685 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLU E 687 " --> pdb=" O ILE E 737 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE E 737 " --> pdb=" O GLU E 687 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N THR E 689 " --> pdb=" O THR E 735 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR E 735 " --> pdb=" O THR E 689 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'E' and resid 29 through 30 removed outlier: 3.597A pdb=" N VAL E 29 " --> pdb=" O SER E 662 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'E' and resid 48 through 56 removed outlier: 7.104A pdb=" N VAL E 566 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP E 52 " --> pdb=" O ILE E 564 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE E 564 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET E 558 " --> pdb=" O LEU E 565 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR E 555 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR E 547 " --> pdb=" O TYR E 555 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY E 557 " --> pdb=" O VAL E 545 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'E' and resid 63 through 70 removed outlier: 3.617A pdb=" N HIS E 98 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'E' and resid 113 through 117 removed outlier: 3.563A pdb=" N ARG E 306 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'E' and resid 132 through 134 removed outlier: 3.517A pdb=" N VAL E 134 " --> pdb=" O GLY E 299 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY E 299 " --> pdb=" O VAL E 134 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'E' and resid 267 through 269 Processing sheet with id=AL7, first strand: chain 'E' and resid 345 through 347 Processing sheet with id=AL8, first strand: chain 'E' and resid 398 through 400 removed outlier: 4.124A pdb=" N HIS E 398 " --> pdb=" O PHE E 409 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU E 406 " --> pdb=" O VAL E 417 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN E 414 " --> pdb=" O THR E 434 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'E' and resid 446 through 447 removed outlier: 6.644A pdb=" N PHE E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'E' and resid 495 through 501 removed outlier: 6.376A pdb=" N ILE E 510 " --> pdb=" O ARG E 496 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE E 498 " --> pdb=" O ALA E 508 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA E 508 " --> pdb=" O ILE E 498 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER E 500 " --> pdb=" O SER E 506 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N SER E 506 " --> pdb=" O SER E 500 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N CYS E 511 " --> pdb=" O SER E 517 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER E 517 " --> pdb=" O CYS E 511 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU E 518 " --> pdb=" O GLN E 537 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLN E 537 " --> pdb=" O LEU E 518 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE E 520 " --> pdb=" O TRP E 535 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TRP E 535 " --> pdb=" O ILE E 520 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ASP E 522 " --> pdb=" O SER E 533 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER E 533 " --> pdb=" O ASP E 522 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU E 524 " --> pdb=" O VAL E 531 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'E' and resid 586 through 593 removed outlier: 6.229A pdb=" N VAL E 587 " --> pdb=" O LEU E 655 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU E 655 " --> pdb=" O VAL E 587 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY E 649 " --> pdb=" O ILE E 593 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE E 616 " --> pdb=" O VAL E 628 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'E' and resid 597 through 599 removed outlier: 6.161A pdb=" N VAL E 639 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE E 633 " --> pdb=" O VAL E 639 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR E 641 " --> pdb=" O GLU E 631 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'E' and resid 706 through 712 removed outlier: 3.625A pdb=" N GLY E 710 " --> pdb=" O ALA E 698 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA E 698 " --> pdb=" O GLY E 710 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.692A pdb=" N ASP F 762 " --> pdb=" O THR F 689 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG F 685 " --> pdb=" O VAL F 766 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN F 768 " --> pdb=" O LEU F 683 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU F 683 " --> pdb=" O GLN F 768 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ARG F 685 " --> pdb=" O VAL F 739 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL F 739 " --> pdb=" O ARG F 685 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLU F 687 " --> pdb=" O ILE F 737 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE F 737 " --> pdb=" O GLU F 687 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N THR F 689 " --> pdb=" O THR F 735 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR F 735 " --> pdb=" O THR F 689 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'F' and resid 29 through 30 removed outlier: 3.597A pdb=" N VAL F 29 " --> pdb=" O SER F 662 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'F' and resid 48 through 56 removed outlier: 7.103A pdb=" N VAL F 566 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP F 52 " --> pdb=" O ILE F 564 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE F 564 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET F 558 " --> pdb=" O LEU F 565 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR F 555 " --> pdb=" O THR F 547 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR F 547 " --> pdb=" O TYR F 555 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY F 557 " --> pdb=" O VAL F 545 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'F' and resid 63 through 70 removed outlier: 3.617A pdb=" N HIS F 98 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'F' and resid 113 through 117 removed outlier: 3.562A pdb=" N ARG F 306 " --> pdb=" O GLU F 316 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'F' and resid 132 through 134 removed outlier: 3.518A pdb=" N VAL F 134 " --> pdb=" O GLY F 299 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY F 299 " --> pdb=" O VAL F 134 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'F' and resid 267 through 269 Processing sheet with id=AN3, first strand: chain 'F' and resid 345 through 347 Processing sheet with id=AN4, first strand: chain 'F' and resid 398 through 400 removed outlier: 4.124A pdb=" N HIS F 398 " --> pdb=" O PHE F 409 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU F 406 " --> pdb=" O VAL F 417 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLN F 414 " --> pdb=" O THR F 434 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'F' and resid 446 through 447 removed outlier: 6.644A pdb=" N PHE F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'F' and resid 495 through 501 removed outlier: 6.377A pdb=" N ILE F 510 " --> pdb=" O ARG F 496 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE F 498 " --> pdb=" O ALA F 508 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA F 508 " --> pdb=" O ILE F 498 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER F 500 " --> pdb=" O SER F 506 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER F 506 " --> pdb=" O SER F 500 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N CYS F 511 " --> pdb=" O SER F 517 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER F 517 " --> pdb=" O CYS F 511 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU F 518 " --> pdb=" O GLN F 537 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN F 537 " --> pdb=" O LEU F 518 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE F 520 " --> pdb=" O TRP F 535 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TRP F 535 " --> pdb=" O ILE F 520 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ASP F 522 " --> pdb=" O SER F 533 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER F 533 " --> pdb=" O ASP F 522 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU F 524 " --> pdb=" O VAL F 531 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'F' and resid 586 through 593 removed outlier: 6.229A pdb=" N VAL F 587 " --> pdb=" O LEU F 655 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU F 655 " --> pdb=" O VAL F 587 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY F 649 " --> pdb=" O ILE F 593 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE F 616 " --> pdb=" O VAL F 628 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'F' and resid 597 through 599 removed outlier: 6.161A pdb=" N VAL F 639 " --> pdb=" O ILE F 633 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE F 633 " --> pdb=" O VAL F 639 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR F 641 " --> pdb=" O GLU F 631 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'F' and resid 706 through 712 removed outlier: 3.625A pdb=" N GLY F 710 " --> pdb=" O ALA F 698 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA F 698 " --> pdb=" O GLY F 710 " (cutoff:3.500A) 1268 hydrogen bonds defined for protein. 3384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.49 Time building geometry restraints manager: 13.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 16586 1.34 - 1.46: 11839 1.46 - 1.58: 22437 1.58 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 51054 Sorted by residual: bond pdb=" N MET P 1 " pdb=" CA MET P 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N MET M 1 " pdb=" CA MET M 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N MET Q 1 " pdb=" CA MET Q 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N MET N 1 " pdb=" CA MET N 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N MET O 1 " pdb=" CA MET O 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 ... (remaining 51049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 66920 1.26 - 2.51: 2334 2.51 - 3.77: 448 3.77 - 5.03: 42 5.03 - 6.29: 12 Bond angle restraints: 69756 Sorted by residual: angle pdb=" C GLN D 71 " pdb=" CA GLN D 71 " pdb=" CB GLN D 71 " ideal model delta sigma weight residual 117.23 111.05 6.18 1.36e+00 5.41e-01 2.07e+01 angle pdb=" C GLN A 71 " pdb=" CA GLN A 71 " pdb=" CB GLN A 71 " ideal model delta sigma weight residual 117.23 111.08 6.15 1.36e+00 5.41e-01 2.04e+01 angle pdb=" C GLN B 71 " pdb=" CA GLN B 71 " pdb=" CB GLN B 71 " ideal model delta sigma weight residual 117.23 111.09 6.14 1.36e+00 5.41e-01 2.04e+01 angle pdb=" C GLN E 71 " pdb=" CA GLN E 71 " pdb=" CB GLN E 71 " ideal model delta sigma weight residual 117.23 111.09 6.14 1.36e+00 5.41e-01 2.04e+01 angle pdb=" C GLN C 71 " pdb=" CA GLN C 71 " pdb=" CB GLN C 71 " ideal model delta sigma weight residual 117.23 111.09 6.14 1.36e+00 5.41e-01 2.03e+01 ... (remaining 69751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 27788 17.61 - 35.22: 1594 35.22 - 52.83: 360 52.83 - 70.43: 60 70.43 - 88.04: 48 Dihedral angle restraints: 29850 sinusoidal: 11034 harmonic: 18816 Sorted by residual: dihedral pdb=" CA PHE C 402 " pdb=" C PHE C 402 " pdb=" N ASN C 403 " pdb=" CA ASN C 403 " ideal model delta harmonic sigma weight residual 180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA PHE D 402 " pdb=" C PHE D 402 " pdb=" N ASN D 403 " pdb=" CA ASN D 403 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA PHE E 402 " pdb=" C PHE E 402 " pdb=" N ASN E 403 " pdb=" CA ASN E 403 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 29847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 4721 0.027 - 0.054: 2196 0.054 - 0.082: 427 0.082 - 0.109: 430 0.109 - 0.136: 356 Chirality restraints: 8130 Sorted by residual: chirality pdb=" CA ILE C 498 " pdb=" N ILE C 498 " pdb=" C ILE C 498 " pdb=" CB ILE C 498 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE D 498 " pdb=" N ILE D 498 " pdb=" C ILE D 498 " pdb=" CB ILE D 498 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE E 498 " pdb=" N ILE E 498 " pdb=" C ILE E 498 " pdb=" CB ILE E 498 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 8127 not shown) Planarity restraints: 9036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 37 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C VAL B 37 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL B 37 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL B 38 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 37 " -0.007 2.00e-02 2.50e+03 1.33e-02 1.78e+00 pdb=" C VAL A 37 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL A 37 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL A 38 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 37 " -0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C VAL F 37 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL F 37 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL F 38 " -0.008 2.00e-02 2.50e+03 ... (remaining 9033 not shown) Histogram of nonbonded interaction distances: 0.36 - 1.27: 84 1.27 - 2.17: 240 2.17 - 3.08: 34131 3.08 - 3.99: 113541 3.99 - 4.90: 220902 Warning: very small nonbonded interaction distances. Nonbonded interactions: 368898 Sorted by model distance: nonbonded pdb=" CA PHE B 3 " pdb=" CZ ARG C 773 " model vdw 0.358 3.700 nonbonded pdb=" CA PHE E 3 " pdb=" CZ ARG F 773 " model vdw 0.358 3.700 nonbonded pdb=" CA PHE C 3 " pdb=" CZ ARG D 773 " model vdw 0.394 3.700 nonbonded pdb=" CZ ARG A 773 " pdb=" CA PHE F 3 " model vdw 0.395 3.700 nonbonded pdb=" CA PHE D 3 " pdb=" CZ ARG E 773 " model vdw 0.403 3.700 ... (remaining 368893 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 2 through 9 or resid 14 through 35 or resid 37 through 42 \ or resid 44 through 56 or resid 65 through 143 or (resid 144 and (name N or name \ CA or name C or name O or name CB )) or resid 145 through 149)) selection = (chain 'H' and (resid 2 through 9 or resid 14 through 35 or resid 37 through 42 \ or resid 44 through 56 or resid 65 through 143 or (resid 144 and (name N or name \ CA or name C or name O or name CB )) or resid 145 through 149)) selection = (chain 'I' and (resid 2 through 9 or resid 14 through 35 or resid 37 through 42 \ or resid 44 through 56 or resid 65 through 143 or (resid 144 and (name N or name \ CA or name C or name O or name CB )) or resid 145 through 149)) selection = (chain 'J' and (resid 2 through 9 or resid 14 through 35 or resid 37 through 42 \ or resid 44 through 56 or resid 65 through 143 or (resid 144 and (name N or name \ CA or name C or name O or name CB )) or resid 145 through 149)) selection = (chain 'K' and (resid 2 through 9 or resid 14 through 35 or resid 37 through 42 \ or resid 44 through 56 or resid 65 through 143 or (resid 144 and (name N or name \ CA or name C or name O or name CB )) or resid 145 through 149)) selection = (chain 'L' and (resid 2 through 9 or resid 14 through 35 or resid 37 through 42 \ or resid 44 through 56 or resid 65 through 143 or (resid 144 and (name N or name \ CA or name C or name O or name CB )) or resid 145 through 149)) selection = (chain 'M' and resid 2 through 149) selection = (chain 'N' and resid 2 through 149) selection = (chain 'O' and resid 2 through 149) selection = (chain 'P' and resid 2 through 149) selection = (chain 'Q' and resid 2 through 149) selection = (chain 'R' and resid 2 through 149) selection = (chain 'S' and (resid 2 through 9 or resid 14 through 35 or resid 37 through 42 \ or resid 44 through 56 or resid 65 through 143 or (resid 144 and (name N or name \ CA or name C or name O or name CB )) or resid 145 through 149)) selection = (chain 'T' and (resid 2 through 9 or resid 14 through 35 or resid 37 through 42 \ or resid 44 through 56 or resid 65 through 143 or (resid 144 and (name N or name \ CA or name C or name O or name CB )) or resid 145 through 149)) selection = (chain 'U' and (resid 2 through 9 or resid 14 through 35 or resid 37 through 42 \ or resid 44 through 56 or resid 65 through 143 or (resid 144 and (name N or name \ CA or name C or name O or name CB )) or resid 145 through 149)) selection = (chain 'V' and (resid 2 through 9 or resid 14 through 35 or resid 37 through 42 \ or resid 44 through 56 or resid 65 through 143 or (resid 144 and (name N or name \ CA or name C or name O or name CB )) or resid 145 through 149)) selection = (chain 'W' and (resid 2 through 9 or resid 14 through 35 or resid 37 through 42 \ or resid 44 through 56 or resid 65 through 143 or (resid 144 and (name N or name \ CA or name C or name O or name CB )) or resid 145 through 149)) selection = (chain 'X' and (resid 2 through 9 or resid 14 through 35 or resid 37 through 42 \ or resid 44 through 56 or resid 65 through 143 or (resid 144 and (name N or name \ CA or name C or name O or name CB )) or resid 145 through 149)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.800 Check model and map are aligned: 0.340 Set scattering table: 0.410 Process input model: 95.910 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 51054 Z= 0.145 Angle : 0.562 6.287 69756 Z= 0.337 Chirality : 0.043 0.136 8130 Planarity : 0.003 0.027 9036 Dihedral : 12.537 88.042 17802 Min Nonbonded Distance : 0.358 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.10), residues: 6378 helix: 0.28 (0.22), residues: 630 sheet: -0.50 (0.12), residues: 1830 loop : -1.41 (0.09), residues: 3918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 548 HIS 0.003 0.001 HIS R 123 PHE 0.010 0.001 PHE O 107 TYR 0.017 0.001 TYR F 686 ARG 0.003 0.000 ARG W 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 774 time to evaluate : 5.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 TYR cc_start: 0.8077 (t80) cc_final: 0.7823 (t80) REVERT: A 381 ASP cc_start: 0.7671 (m-30) cc_final: 0.7370 (t0) REVERT: A 745 ASP cc_start: 0.7464 (t0) cc_final: 0.6748 (t70) REVERT: R 33 ASN cc_start: 0.7970 (m-40) cc_final: 0.7747 (m110) REVERT: Q 32 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7928 (ttp80) REVERT: Q 122 MET cc_start: 0.8751 (mmm) cc_final: 0.8387 (tpp) REVERT: P 1 MET cc_start: 0.8219 (mmt) cc_final: 0.7810 (mmt) REVERT: P 77 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7665 (mtp-110) REVERT: P 109 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7107 (mt-10) REVERT: N 32 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7925 (ttp80) REVERT: N 122 MET cc_start: 0.8747 (mmm) cc_final: 0.8386 (tpp) REVERT: M 1 MET cc_start: 0.8219 (mmt) cc_final: 0.7809 (mmt) REVERT: M 77 ARG cc_start: 0.8032 (mtp-110) cc_final: 0.7658 (mtp-110) REVERT: M 109 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7108 (mt-10) REVERT: X 130 LEU cc_start: 0.8072 (tp) cc_final: 0.7843 (tt) REVERT: W 35 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7629 (mm-30) REVERT: U 130 LEU cc_start: 0.8056 (tp) cc_final: 0.7827 (tt) REVERT: T 35 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7633 (mm-30) REVERT: L 28 ILE cc_start: 0.8994 (mm) cc_final: 0.8680 (mm) REVERT: L 118 PHE cc_start: 0.6852 (m-80) cc_final: 0.6505 (m-80) REVERT: J 142 LYS cc_start: 0.7281 (ttpp) cc_final: 0.7042 (ttpt) REVERT: I 28 ILE cc_start: 0.8991 (mm) cc_final: 0.8653 (mm) REVERT: I 118 PHE cc_start: 0.6845 (m-80) cc_final: 0.6497 (m-80) REVERT: G 142 LYS cc_start: 0.7279 (ttpp) cc_final: 0.7035 (ttpt) REVERT: B 281 TYR cc_start: 0.8168 (t80) cc_final: 0.7895 (t80) REVERT: B 381 ASP cc_start: 0.7436 (m-30) cc_final: 0.7157 (t0) REVERT: B 608 VAL cc_start: 0.9060 (p) cc_final: 0.8855 (t) REVERT: B 650 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7300 (mm-30) REVERT: B 674 ILE cc_start: 0.8604 (mm) cc_final: 0.8345 (mm) REVERT: B 745 ASP cc_start: 0.7323 (t0) cc_final: 0.6853 (t70) REVERT: C 381 ASP cc_start: 0.7614 (m-30) cc_final: 0.7229 (t0) REVERT: C 745 ASP cc_start: 0.7210 (t0) cc_final: 0.6729 (t0) REVERT: D 281 TYR cc_start: 0.8073 (t80) cc_final: 0.7817 (t80) REVERT: D 381 ASP cc_start: 0.7664 (m-30) cc_final: 0.7366 (t0) REVERT: D 745 ASP cc_start: 0.7462 (t0) cc_final: 0.6747 (t70) REVERT: E 281 TYR cc_start: 0.8170 (t80) cc_final: 0.7898 (t80) REVERT: E 381 ASP cc_start: 0.7435 (m-30) cc_final: 0.7159 (t0) REVERT: E 608 VAL cc_start: 0.9058 (p) cc_final: 0.8854 (t) REVERT: E 650 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7298 (mm-30) REVERT: E 674 ILE cc_start: 0.8603 (mm) cc_final: 0.8344 (mm) REVERT: E 745 ASP cc_start: 0.7326 (t0) cc_final: 0.6856 (t70) REVERT: F 381 ASP cc_start: 0.7615 (m-30) cc_final: 0.7227 (t0) REVERT: F 745 ASP cc_start: 0.7212 (t0) cc_final: 0.6724 (t0) outliers start: 0 outliers final: 0 residues processed: 774 average time/residue: 0.5897 time to fit residues: 763.1316 Evaluate side-chains 604 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 604 time to evaluate : 5.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 537 optimal weight: 0.0040 chunk 482 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 325 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 498 optimal weight: 6.9990 chunk 192 optimal weight: 0.0000 chunk 303 optimal weight: 0.8980 chunk 371 optimal weight: 5.9990 chunk 577 optimal weight: 10.0000 overall best weight: 2.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 149 ASN Q 72 ASN Q 149 ASN P 5 GLN P 33 ASN P 123 HIS P 149 ASN O 149 ASN N 72 ASN N 149 ASN M 5 GLN M 149 ASN X 123 HIS W 46 GLN W 123 HIS U 123 HIS T 46 GLN T 123 HIS J 46 GLN G 46 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 51054 Z= 0.302 Angle : 0.657 15.329 69756 Z= 0.355 Chirality : 0.049 0.163 8130 Planarity : 0.006 0.166 9036 Dihedral : 4.852 33.460 7122 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.43 % Allowed : 6.24 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.10), residues: 6378 helix: 0.08 (0.21), residues: 642 sheet: -0.26 (0.12), residues: 1968 loop : -1.50 (0.09), residues: 3768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 548 HIS 0.004 0.001 HIS B 98 PHE 0.023 0.002 PHE N 107 TYR 0.024 0.002 TYR E 686 ARG 0.016 0.001 ARG T 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 617 time to evaluate : 5.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 TYR cc_start: 0.8138 (t80) cc_final: 0.7883 (t80) REVERT: A 381 ASP cc_start: 0.7785 (m-30) cc_final: 0.7343 (t0) REVERT: A 745 ASP cc_start: 0.7550 (t0) cc_final: 0.6824 (t70) REVERT: Q 122 MET cc_start: 0.8681 (mmm) cc_final: 0.8474 (mmm) REVERT: P 109 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7354 (mt-10) REVERT: P 117 TYR cc_start: 0.8253 (m-10) cc_final: 0.8040 (m-10) REVERT: N 122 MET cc_start: 0.8681 (mmm) cc_final: 0.8476 (mmm) REVERT: M 109 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7357 (mt-10) REVERT: M 117 TYR cc_start: 0.8255 (m-10) cc_final: 0.8040 (m-10) REVERT: X 130 LEU cc_start: 0.8388 (tp) cc_final: 0.8077 (tt) REVERT: U 130 LEU cc_start: 0.8393 (tp) cc_final: 0.8084 (tt) REVERT: L 28 ILE cc_start: 0.9161 (mm) cc_final: 0.8952 (mm) REVERT: I 28 ILE cc_start: 0.9071 (mm) cc_final: 0.8846 (mm) REVERT: I 35 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8126 (mt-10) REVERT: B 281 TYR cc_start: 0.8219 (t80) cc_final: 0.7994 (t80) REVERT: B 381 ASP cc_start: 0.7574 (m-30) cc_final: 0.7142 (t0) REVERT: C 381 ASP cc_start: 0.7737 (m-30) cc_final: 0.7187 (t0) REVERT: C 745 ASP cc_start: 0.7355 (t0) cc_final: 0.6779 (t0) REVERT: D 281 TYR cc_start: 0.8134 (t80) cc_final: 0.7878 (t80) REVERT: D 381 ASP cc_start: 0.7779 (m-30) cc_final: 0.7332 (t0) REVERT: D 745 ASP cc_start: 0.7554 (t0) cc_final: 0.6828 (t70) REVERT: E 281 TYR cc_start: 0.8217 (t80) cc_final: 0.7993 (t80) REVERT: E 381 ASP cc_start: 0.7573 (m-30) cc_final: 0.7141 (t0) REVERT: F 381 ASP cc_start: 0.7741 (m-30) cc_final: 0.7188 (t0) REVERT: F 745 ASP cc_start: 0.7355 (t0) cc_final: 0.6780 (t0) outliers start: 76 outliers final: 50 residues processed: 655 average time/residue: 0.5928 time to fit residues: 656.3553 Evaluate side-chains 576 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 526 time to evaluate : 5.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 118 PHE Chi-restraints excluded: chain O residue 118 PHE Chi-restraints excluded: chain N residue 3 SER Chi-restraints excluded: chain N residue 145 VAL Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 118 PHE Chi-restraints excluded: chain X residue 9 SER Chi-restraints excluded: chain X residue 83 ASP Chi-restraints excluded: chain W residue 83 ASP Chi-restraints excluded: chain W residue 130 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain T residue 83 ASP Chi-restraints excluded: chain T residue 130 LEU Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 526 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 320 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 480 optimal weight: 0.9980 chunk 393 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 578 optimal weight: 8.9990 chunk 625 optimal weight: 0.0980 chunk 515 optimal weight: 10.0000 chunk 573 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 464 optimal weight: 9.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 54 ASN Q 33 ASN N 33 ASN X 143 GLN W 46 GLN W 143 GLN V 143 GLN U 143 GLN T 46 GLN T 143 GLN S 143 GLN J 46 GLN G 46 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 51054 Z= 0.314 Angle : 0.619 9.148 69756 Z= 0.335 Chirality : 0.049 0.161 8130 Planarity : 0.004 0.031 9036 Dihedral : 5.027 39.667 7122 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.11 % Favored : 93.87 % Rotamer: Outliers : 2.62 % Allowed : 7.98 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.10), residues: 6378 helix: 0.02 (0.21), residues: 648 sheet: -0.14 (0.12), residues: 1938 loop : -1.61 (0.09), residues: 3792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 548 HIS 0.004 0.001 HIS E 536 PHE 0.022 0.002 PHE Q 107 TYR 0.023 0.002 TYR A 686 ARG 0.006 0.001 ARG P 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 543 time to evaluate : 5.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 745 ASP cc_start: 0.7780 (t0) cc_final: 0.7058 (t70) REVERT: Q 77 ARG cc_start: 0.8653 (mtp-110) cc_final: 0.8423 (mtp-110) REVERT: Q 122 MET cc_start: 0.8928 (mmm) cc_final: 0.8220 (tpp) REVERT: P 117 TYR cc_start: 0.8363 (m-10) cc_final: 0.8090 (m-10) REVERT: O 77 ARG cc_start: 0.8264 (mtp-110) cc_final: 0.7970 (mtp-110) REVERT: N 77 ARG cc_start: 0.8653 (mtp-110) cc_final: 0.8423 (mtp-110) REVERT: N 122 MET cc_start: 0.8927 (mmm) cc_final: 0.8217 (tpp) REVERT: M 117 TYR cc_start: 0.8361 (m-10) cc_final: 0.8090 (m-10) REVERT: X 130 LEU cc_start: 0.8438 (tp) cc_final: 0.8076 (tt) REVERT: W 100 MET cc_start: 0.8443 (tpt) cc_final: 0.8166 (tpt) REVERT: U 130 LEU cc_start: 0.8443 (tp) cc_final: 0.8080 (tt) REVERT: T 100 MET cc_start: 0.8444 (tpt) cc_final: 0.8170 (tpt) REVERT: L 50 ASP cc_start: 0.7102 (m-30) cc_final: 0.6887 (m-30) REVERT: I 50 ASP cc_start: 0.7048 (m-30) cc_final: 0.6847 (m-30) REVERT: B 381 ASP cc_start: 0.7725 (m-30) cc_final: 0.6981 (t0) REVERT: C 381 ASP cc_start: 0.7785 (m-30) cc_final: 0.7199 (t0) REVERT: C 674 ILE cc_start: 0.8677 (mm) cc_final: 0.8188 (mt) REVERT: D 745 ASP cc_start: 0.7779 (t0) cc_final: 0.7053 (t70) REVERT: E 381 ASP cc_start: 0.7725 (m-30) cc_final: 0.6979 (t0) REVERT: F 381 ASP cc_start: 0.7785 (m-30) cc_final: 0.7199 (t0) REVERT: F 674 ILE cc_start: 0.8678 (mm) cc_final: 0.8190 (mt) outliers start: 139 outliers final: 90 residues processed: 645 average time/residue: 0.5818 time to fit residues: 643.2364 Evaluate side-chains 605 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 515 time to evaluate : 5.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 118 PHE Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain N residue 3 SER Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 118 PHE Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain X residue 9 SER Chi-restraints excluded: chain X residue 29 THR Chi-restraints excluded: chain X residue 83 ASP Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 83 ASP Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 130 LEU Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain U residue 29 THR Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 83 ASP Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 126 GLN Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 676 ILE Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 476 SER Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 653 VAL Chi-restraints excluded: chain F residue 747 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 571 optimal weight: 5.9990 chunk 435 optimal weight: 1.9990 chunk 300 optimal weight: 0.0770 chunk 64 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 chunk 388 optimal weight: 10.0000 chunk 580 optimal weight: 9.9990 chunk 614 optimal weight: 3.9990 chunk 303 optimal weight: 10.0000 chunk 550 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 51054 Z= 0.206 Angle : 0.546 7.916 69756 Z= 0.296 Chirality : 0.047 0.152 8130 Planarity : 0.004 0.032 9036 Dihedral : 4.740 33.646 7122 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.85 % Rotamer: Outliers : 2.36 % Allowed : 9.63 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.10), residues: 6378 helix: 0.20 (0.21), residues: 648 sheet: -0.01 (0.12), residues: 1914 loop : -1.63 (0.09), residues: 3816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 548 HIS 0.004 0.001 HIS D 536 PHE 0.020 0.001 PHE N 107 TYR 0.016 0.001 TYR D 686 ARG 0.005 0.000 ARG R 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 549 time to evaluate : 5.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 558 MET cc_start: 0.8740 (mtm) cc_final: 0.8519 (mtp) REVERT: A 745 ASP cc_start: 0.7920 (t0) cc_final: 0.7278 (t70) REVERT: R 77 ARG cc_start: 0.8253 (mtp-110) cc_final: 0.7866 (ptm-80) REVERT: Q 77 ARG cc_start: 0.8619 (mtp-110) cc_final: 0.8418 (mtp-110) REVERT: P 48 ASP cc_start: 0.6585 (p0) cc_final: 0.6171 (p0) REVERT: P 117 TYR cc_start: 0.8399 (m-10) cc_final: 0.8137 (m-10) REVERT: O 77 ARG cc_start: 0.8244 (mtp-110) cc_final: 0.7825 (ptm-80) REVERT: N 77 ARG cc_start: 0.8621 (mtp-110) cc_final: 0.8420 (mtp-110) REVERT: M 48 ASP cc_start: 0.6589 (p0) cc_final: 0.6166 (p0) REVERT: M 117 TYR cc_start: 0.8401 (m-10) cc_final: 0.8139 (m-10) REVERT: X 83 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: W 100 MET cc_start: 0.8482 (tpt) cc_final: 0.8151 (tpt) REVERT: U 83 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: T 100 MET cc_start: 0.8486 (tpt) cc_final: 0.8152 (tpt) REVERT: L 50 ASP cc_start: 0.7037 (m-30) cc_final: 0.6813 (m-30) REVERT: L 146 ASP cc_start: 0.7292 (m-30) cc_final: 0.7029 (m-30) REVERT: K 146 ASP cc_start: 0.7668 (m-30) cc_final: 0.7294 (m-30) REVERT: I 50 ASP cc_start: 0.6968 (m-30) cc_final: 0.6734 (m-30) REVERT: B 381 ASP cc_start: 0.7677 (m-30) cc_final: 0.6887 (t0) REVERT: B 528 ASP cc_start: 0.7953 (t0) cc_final: 0.7690 (t0) REVERT: C 381 ASP cc_start: 0.7751 (m-30) cc_final: 0.7176 (t0) REVERT: C 674 ILE cc_start: 0.8678 (mm) cc_final: 0.8205 (mt) REVERT: D 558 MET cc_start: 0.8740 (mtm) cc_final: 0.8513 (mtp) REVERT: D 745 ASP cc_start: 0.7916 (t0) cc_final: 0.7272 (t70) REVERT: E 381 ASP cc_start: 0.7674 (m-30) cc_final: 0.6883 (t0) REVERT: E 528 ASP cc_start: 0.7961 (t0) cc_final: 0.7697 (t0) REVERT: F 381 ASP cc_start: 0.7753 (m-30) cc_final: 0.7178 (t0) REVERT: F 674 ILE cc_start: 0.8680 (mm) cc_final: 0.8208 (mt) outliers start: 125 outliers final: 68 residues processed: 640 average time/residue: 0.5837 time to fit residues: 634.5205 Evaluate side-chains 597 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 527 time to evaluate : 5.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain O residue 118 PHE Chi-restraints excluded: chain N residue 3 SER Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain X residue 9 SER Chi-restraints excluded: chain X residue 83 ASP Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 83 ASP Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 130 LEU Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 83 ASP Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 126 GLN Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 126 GLN Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 721 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 476 SER Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 721 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 511 optimal weight: 7.9990 chunk 348 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 457 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 524 optimal weight: 8.9990 chunk 424 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 313 optimal weight: 1.9990 chunk 551 optimal weight: 7.9990 chunk 155 optimal weight: 0.4980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 54 ASN N 72 ASN M 54 ASN V 143 GLN S 143 GLN D 536 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 51054 Z= 0.202 Angle : 0.545 13.089 69756 Z= 0.293 Chirality : 0.046 0.151 8130 Planarity : 0.004 0.032 9036 Dihedral : 4.621 31.316 7122 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.06 % Rotamer: Outliers : 2.83 % Allowed : 9.86 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.10), residues: 6378 helix: 0.33 (0.21), residues: 648 sheet: 0.08 (0.12), residues: 1854 loop : -1.60 (0.09), residues: 3876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 548 HIS 0.004 0.001 HIS D 536 PHE 0.020 0.001 PHE Q 107 TYR 0.015 0.001 TYR D 686 ARG 0.004 0.000 ARG N 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 555 time to evaluate : 5.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 745 ASP cc_start: 0.7937 (t0) cc_final: 0.7222 (t70) REVERT: R 83 ASP cc_start: 0.8063 (t0) cc_final: 0.7531 (t0) REVERT: Q 77 ARG cc_start: 0.8625 (mtp-110) cc_final: 0.8415 (mtp-110) REVERT: Q 122 MET cc_start: 0.8750 (mmm) cc_final: 0.8438 (mmm) REVERT: P 117 TYR cc_start: 0.8433 (m-10) cc_final: 0.8152 (m-10) REVERT: O 77 ARG cc_start: 0.8253 (mtp-110) cc_final: 0.7837 (ptm-80) REVERT: N 77 ARG cc_start: 0.8629 (mtp-110) cc_final: 0.8417 (mtp-110) REVERT: N 122 MET cc_start: 0.8751 (mmm) cc_final: 0.8436 (mmm) REVERT: M 117 TYR cc_start: 0.8435 (m-10) cc_final: 0.8155 (m-10) REVERT: X 29 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8548 (m) REVERT: X 83 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: W 100 MET cc_start: 0.8425 (tpt) cc_final: 0.8187 (tpt) REVERT: V 149 ASN cc_start: 0.6835 (m-40) cc_final: 0.6386 (m-40) REVERT: U 29 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8547 (m) REVERT: U 83 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: T 100 MET cc_start: 0.8431 (tpt) cc_final: 0.8193 (tpt) REVERT: L 50 ASP cc_start: 0.7080 (m-30) cc_final: 0.6853 (m-30) REVERT: L 146 ASP cc_start: 0.7393 (m-30) cc_final: 0.7172 (m-30) REVERT: K 146 ASP cc_start: 0.7715 (m-30) cc_final: 0.7322 (m-30) REVERT: J 126 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: I 50 ASP cc_start: 0.7078 (m-30) cc_final: 0.6850 (m-30) REVERT: I 146 ASP cc_start: 0.7520 (m-30) cc_final: 0.7202 (m-30) REVERT: H 146 ASP cc_start: 0.7714 (m-30) cc_final: 0.7321 (m-30) REVERT: B 381 ASP cc_start: 0.7672 (m-30) cc_final: 0.6812 (t0) REVERT: B 528 ASP cc_start: 0.7902 (t0) cc_final: 0.7625 (t0) REVERT: B 674 ILE cc_start: 0.8876 (mm) cc_final: 0.8655 (mm) REVERT: C 674 ILE cc_start: 0.8671 (mm) cc_final: 0.8171 (mt) REVERT: D 745 ASP cc_start: 0.7933 (t0) cc_final: 0.7217 (t70) REVERT: E 381 ASP cc_start: 0.7672 (m-30) cc_final: 0.6811 (t0) REVERT: E 528 ASP cc_start: 0.7908 (t0) cc_final: 0.7626 (t0) REVERT: E 674 ILE cc_start: 0.8876 (mm) cc_final: 0.8654 (mm) REVERT: F 674 ILE cc_start: 0.8699 (mm) cc_final: 0.8212 (mt) outliers start: 150 outliers final: 109 residues processed: 667 average time/residue: 0.5709 time to fit residues: 659.7643 Evaluate side-chains 654 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 540 time to evaluate : 5.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 118 PHE Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 118 PHE Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain N residue 3 SER Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 118 PHE Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain X residue 9 SER Chi-restraints excluded: chain X residue 29 THR Chi-restraints excluded: chain X residue 34 LEU Chi-restraints excluded: chain X residue 83 ASP Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 130 LEU Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain U residue 29 THR Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 126 GLN Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 126 GLN Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 721 GLU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 664 THR Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 476 SER Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 653 VAL Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 721 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 206 optimal weight: 7.9990 chunk 553 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 360 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 615 optimal weight: 2.9990 chunk 510 optimal weight: 10.0000 chunk 284 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 323 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 HIS R 46 GLN R 123 HIS Q 46 GLN Q 72 ASN Q 149 ASN P 46 GLN N 46 GLN N 149 ASN M 46 GLN B 536 HIS C 536 HIS E 12 GLN F 536 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 51054 Z= 0.455 Angle : 0.691 12.815 69756 Z= 0.371 Chirality : 0.052 0.175 8130 Planarity : 0.005 0.036 9036 Dihedral : 5.255 37.981 7122 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.93 % Favored : 91.97 % Rotamer: Outliers : 3.51 % Allowed : 10.97 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.10), residues: 6378 helix: 0.01 (0.20), residues: 654 sheet: -0.14 (0.12), residues: 1980 loop : -1.85 (0.09), residues: 3744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 548 HIS 0.008 0.002 HIS D 536 PHE 0.023 0.002 PHE N 107 TYR 0.022 0.002 TYR D 686 ARG 0.006 0.001 ARG A 596 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 538 time to evaluate : 5.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 674 ILE cc_start: 0.8759 (mm) cc_final: 0.8456 (mt) REVERT: A 745 ASP cc_start: 0.8141 (t0) cc_final: 0.7415 (t70) REVERT: R 32 ARG cc_start: 0.7846 (ttp-110) cc_final: 0.7626 (ttp-110) REVERT: R 83 ASP cc_start: 0.8254 (t0) cc_final: 0.7696 (t0) REVERT: Q 77 ARG cc_start: 0.8677 (mtp-110) cc_final: 0.8466 (mtp-110) REVERT: P 54 ASN cc_start: 0.8026 (m-40) cc_final: 0.7555 (m-40) REVERT: P 117 TYR cc_start: 0.8443 (m-10) cc_final: 0.8140 (m-10) REVERT: O 83 ASP cc_start: 0.8198 (t0) cc_final: 0.7654 (t0) REVERT: N 77 ARG cc_start: 0.8684 (mtp-110) cc_final: 0.8468 (mtp-110) REVERT: M 54 ASN cc_start: 0.8020 (m-40) cc_final: 0.7552 (m-40) REVERT: M 117 TYR cc_start: 0.8444 (m-10) cc_final: 0.8140 (m-10) REVERT: X 83 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: W 100 MET cc_start: 0.8510 (tpt) cc_final: 0.8089 (tpt) REVERT: V 149 ASN cc_start: 0.7068 (m-40) cc_final: 0.6734 (m-40) REVERT: U 83 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: U 122 MET cc_start: 0.8708 (mmm) cc_final: 0.7833 (tpt) REVERT: T 100 MET cc_start: 0.8520 (tpt) cc_final: 0.8090 (tpt) REVERT: S 149 ASN cc_start: 0.7072 (m-40) cc_final: 0.6736 (m-40) REVERT: L 146 ASP cc_start: 0.7597 (m-30) cc_final: 0.7261 (m-30) REVERT: J 126 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: G 126 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8003 (mt0) REVERT: B 528 ASP cc_start: 0.7888 (t0) cc_final: 0.7561 (t0) REVERT: C 674 ILE cc_start: 0.8706 (mm) cc_final: 0.8215 (mt) REVERT: D 674 ILE cc_start: 0.8812 (mm) cc_final: 0.8510 (mt) REVERT: D 745 ASP cc_start: 0.8140 (t0) cc_final: 0.7412 (t70) REVERT: E 528 ASP cc_start: 0.7896 (t0) cc_final: 0.7571 (t0) REVERT: F 674 ILE cc_start: 0.8709 (mm) cc_final: 0.8216 (mt) outliers start: 186 outliers final: 150 residues processed: 687 average time/residue: 0.5729 time to fit residues: 676.4925 Evaluate side-chains 660 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 506 time to evaluate : 5.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 118 PHE Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain N residue 3 SER Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 48 ASP Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain X residue 9 SER Chi-restraints excluded: chain X residue 29 THR Chi-restraints excluded: chain X residue 83 ASP Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 130 LEU Chi-restraints excluded: chain V residue 140 VAL Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain U residue 29 THR Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 83 ASP Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 70 ARG Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 126 GLN Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 126 GLN Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 721 GLU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 664 THR Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 476 SER Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 653 VAL Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 721 GLU Chi-restraints excluded: chain F residue 747 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 593 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 350 optimal weight: 3.9990 chunk 449 optimal weight: 5.9990 chunk 348 optimal weight: 0.9980 chunk 518 optimal weight: 4.9990 chunk 343 optimal weight: 2.9990 chunk 613 optimal weight: 4.9990 chunk 383 optimal weight: 4.9990 chunk 373 optimal weight: 6.9990 chunk 283 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN Q 46 GLN Q 129 ASN O 123 HIS N 129 ASN M 123 HIS M 149 ASN D 30 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 51054 Z= 0.292 Angle : 0.605 11.767 69756 Z= 0.326 Chirality : 0.048 0.168 8130 Planarity : 0.004 0.035 9036 Dihedral : 5.009 35.541 7122 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.44 % Favored : 93.46 % Rotamer: Outliers : 3.34 % Allowed : 11.58 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.10), residues: 6378 helix: 0.26 (0.21), residues: 654 sheet: -0.05 (0.12), residues: 1920 loop : -1.88 (0.09), residues: 3804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 548 HIS 0.006 0.001 HIS D 536 PHE 0.022 0.002 PHE N 107 TYR 0.016 0.002 TYR B 588 ARG 0.004 0.000 ARG M 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 544 time to evaluate : 5.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 745 ASP cc_start: 0.8069 (t0) cc_final: 0.7392 (t70) REVERT: R 83 ASP cc_start: 0.8212 (t0) cc_final: 0.7575 (t0) REVERT: Q 53 ILE cc_start: 0.9011 (mm) cc_final: 0.8733 (mm) REVERT: Q 77 ARG cc_start: 0.8639 (mtp-110) cc_final: 0.8425 (mtp-110) REVERT: P 54 ASN cc_start: 0.8041 (m-40) cc_final: 0.7713 (m-40) REVERT: P 83 ASP cc_start: 0.8385 (t0) cc_final: 0.8148 (t0) REVERT: P 117 TYR cc_start: 0.8568 (m-10) cc_final: 0.8328 (m-10) REVERT: O 48 ASP cc_start: 0.6588 (p0) cc_final: 0.6278 (p0) REVERT: O 83 ASP cc_start: 0.8189 (t0) cc_final: 0.7593 (t0) REVERT: N 53 ILE cc_start: 0.9011 (mm) cc_final: 0.8770 (mm) REVERT: N 77 ARG cc_start: 0.8643 (mtp-110) cc_final: 0.8428 (mtp-110) REVERT: M 54 ASN cc_start: 0.8045 (m-40) cc_final: 0.7718 (m-40) REVERT: M 83 ASP cc_start: 0.8376 (t0) cc_final: 0.8149 (t0) REVERT: M 117 TYR cc_start: 0.8569 (m-10) cc_final: 0.8326 (m-10) REVERT: X 83 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: W 100 MET cc_start: 0.8525 (tpt) cc_final: 0.8211 (tpt) REVERT: V 122 MET cc_start: 0.8544 (tpt) cc_final: 0.7705 (tpp) REVERT: V 149 ASN cc_start: 0.7028 (m-40) cc_final: 0.6762 (m-40) REVERT: U 83 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: U 122 MET cc_start: 0.8562 (mmm) cc_final: 0.8126 (tpp) REVERT: T 100 MET cc_start: 0.8536 (tpt) cc_final: 0.8119 (tpt) REVERT: S 122 MET cc_start: 0.8548 (tpt) cc_final: 0.7717 (tpp) REVERT: S 149 ASN cc_start: 0.7119 (m-40) cc_final: 0.6863 (m-40) REVERT: L 146 ASP cc_start: 0.7536 (m-30) cc_final: 0.7193 (m-30) REVERT: J 126 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: G 126 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7893 (mt0) REVERT: B 528 ASP cc_start: 0.7879 (t0) cc_final: 0.7563 (t0) REVERT: C 674 ILE cc_start: 0.8666 (mm) cc_final: 0.8172 (mt) REVERT: D 745 ASP cc_start: 0.8071 (t0) cc_final: 0.7392 (t70) REVERT: E 528 ASP cc_start: 0.7885 (t0) cc_final: 0.7571 (t0) REVERT: E 674 ILE cc_start: 0.8824 (mm) cc_final: 0.8513 (mt) REVERT: F 674 ILE cc_start: 0.8669 (mm) cc_final: 0.8175 (mt) outliers start: 177 outliers final: 142 residues processed: 676 average time/residue: 0.5635 time to fit residues: 658.6410 Evaluate side-chains 669 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 523 time to evaluate : 5.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain N residue 3 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 48 ASP Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain X residue 9 SER Chi-restraints excluded: chain X residue 29 THR Chi-restraints excluded: chain X residue 34 LEU Chi-restraints excluded: chain X residue 83 ASP Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 130 LEU Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain U residue 29 THR Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 83 ASP Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 70 ARG Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 126 GLN Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 126 GLN Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 721 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 664 THR Chi-restraints excluded: chain E residue 676 ILE Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 476 SER Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 653 VAL Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 721 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 379 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 366 optimal weight: 0.0020 chunk 184 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 118 optimal weight: 8.9990 chunk 389 optimal weight: 0.2980 chunk 417 optimal weight: 0.7980 chunk 303 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 481 optimal weight: 5.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 46 GLN Q 46 GLN ** Q 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 129 ASN P 46 GLN O 46 GLN N 46 GLN N 129 ASN M 46 GLN M 149 ASN B 414 GLN C 30 GLN C 414 GLN D 414 GLN E 414 GLN F 30 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 51054 Z= 0.125 Angle : 0.511 10.192 69756 Z= 0.275 Chirality : 0.044 0.147 8130 Planarity : 0.003 0.034 9036 Dihedral : 4.377 26.055 7122 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % Rotamer: Outliers : 2.00 % Allowed : 13.24 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.10), residues: 6378 helix: 0.66 (0.22), residues: 648 sheet: 0.21 (0.12), residues: 1944 loop : -1.74 (0.09), residues: 3786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 47 HIS 0.004 0.001 HIS E 536 PHE 0.020 0.001 PHE Q 107 TYR 0.013 0.001 TYR C 49 ARG 0.004 0.000 ARG N 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 577 time to evaluate : 5.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 674 ILE cc_start: 0.8382 (mm) cc_final: 0.8078 (mm) REVERT: A 745 ASP cc_start: 0.7910 (t0) cc_final: 0.7263 (t70) REVERT: R 83 ASP cc_start: 0.8201 (t0) cc_final: 0.7631 (t0) REVERT: Q 77 ARG cc_start: 0.8626 (mtp-110) cc_final: 0.8394 (mtp-110) REVERT: Q 122 MET cc_start: 0.8724 (mmm) cc_final: 0.8505 (mmm) REVERT: P 54 ASN cc_start: 0.8060 (m-40) cc_final: 0.7549 (m-40) REVERT: P 117 TYR cc_start: 0.8514 (m-10) cc_final: 0.8269 (m-10) REVERT: O 83 ASP cc_start: 0.8173 (t0) cc_final: 0.7599 (t0) REVERT: N 53 ILE cc_start: 0.8867 (mm) cc_final: 0.8648 (mm) REVERT: N 77 ARG cc_start: 0.8633 (mtp-110) cc_final: 0.8397 (mtp-110) REVERT: N 122 MET cc_start: 0.8725 (mmm) cc_final: 0.8509 (mmm) REVERT: M 54 ASN cc_start: 0.8055 (m-40) cc_final: 0.7547 (m-40) REVERT: M 117 TYR cc_start: 0.8515 (m-10) cc_final: 0.8269 (m-10) REVERT: X 83 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: W 100 MET cc_start: 0.8466 (tpt) cc_final: 0.8136 (tpt) REVERT: V 122 MET cc_start: 0.8450 (tpt) cc_final: 0.7651 (tpp) REVERT: V 149 ASN cc_start: 0.7039 (m-40) cc_final: 0.6751 (m-40) REVERT: U 83 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: U 122 MET cc_start: 0.8225 (mmm) cc_final: 0.7714 (tpp) REVERT: T 100 MET cc_start: 0.8468 (tpt) cc_final: 0.8139 (tpt) REVERT: S 122 MET cc_start: 0.8455 (tpt) cc_final: 0.7661 (tpp) REVERT: S 149 ASN cc_start: 0.7042 (m-40) cc_final: 0.6753 (m-40) REVERT: L 146 ASP cc_start: 0.7364 (m-30) cc_final: 0.7113 (m-30) REVERT: K 146 ASP cc_start: 0.7576 (m-30) cc_final: 0.7124 (m-30) REVERT: J 126 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: H 146 ASP cc_start: 0.7580 (m-30) cc_final: 0.7131 (m-30) REVERT: G 126 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: B 281 TYR cc_start: 0.8108 (t80) cc_final: 0.7700 (t80) REVERT: B 528 ASP cc_start: 0.7829 (t0) cc_final: 0.7539 (t0) REVERT: B 674 ILE cc_start: 0.8712 (mm) cc_final: 0.8512 (mm) REVERT: C 674 ILE cc_start: 0.8704 (mm) cc_final: 0.8387 (mt) REVERT: D 745 ASP cc_start: 0.7906 (t0) cc_final: 0.7260 (t70) REVERT: E 281 TYR cc_start: 0.8114 (t80) cc_final: 0.7703 (t80) REVERT: E 528 ASP cc_start: 0.7834 (t0) cc_final: 0.7542 (t0) REVERT: E 674 ILE cc_start: 0.8715 (mm) cc_final: 0.8514 (mm) REVERT: F 674 ILE cc_start: 0.8707 (mm) cc_final: 0.8391 (mt) outliers start: 106 outliers final: 81 residues processed: 656 average time/residue: 0.5907 time to fit residues: 664.1680 Evaluate side-chains 611 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 526 time to evaluate : 5.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 118 PHE Chi-restraints excluded: chain O residue 118 PHE Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 48 ASP Chi-restraints excluded: chain M residue 118 PHE Chi-restraints excluded: chain X residue 9 SER Chi-restraints excluded: chain X residue 83 ASP Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 126 GLN Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 126 GLN Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 721 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 721 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 557 optimal weight: 10.0000 chunk 587 optimal weight: 0.7980 chunk 535 optimal weight: 6.9990 chunk 571 optimal weight: 0.9990 chunk 343 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 448 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 516 optimal weight: 0.9990 chunk 540 optimal weight: 1.9990 chunk 569 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN ** Q 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 129 ASN ** P 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN M 149 ASN I 54 ASN C 30 GLN F 30 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 51054 Z= 0.149 Angle : 0.522 10.144 69756 Z= 0.279 Chirality : 0.045 0.170 8130 Planarity : 0.004 0.033 9036 Dihedral : 4.288 25.318 7122 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.75 % Favored : 94.15 % Rotamer: Outliers : 2.17 % Allowed : 13.54 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.10), residues: 6378 helix: 0.62 (0.22), residues: 654 sheet: 0.28 (0.12), residues: 1944 loop : -1.69 (0.09), residues: 3780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Q 47 HIS 0.004 0.001 HIS E 536 PHE 0.018 0.001 PHE Q 107 TYR 0.013 0.001 TYR B 49 ARG 0.006 0.000 ARG R 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 535 time to evaluate : 5.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 674 ILE cc_start: 0.8478 (mm) cc_final: 0.8185 (mm) REVERT: A 745 ASP cc_start: 0.7897 (t0) cc_final: 0.7245 (t70) REVERT: R 83 ASP cc_start: 0.8211 (t0) cc_final: 0.7653 (t0) REVERT: Q 48 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7158 (p0) REVERT: Q 77 ARG cc_start: 0.8604 (mtp-110) cc_final: 0.8129 (ptm160) REVERT: Q 122 MET cc_start: 0.8673 (mmm) cc_final: 0.8424 (mmm) REVERT: P 54 ASN cc_start: 0.7972 (m-40) cc_final: 0.7641 (m-40) REVERT: P 117 TYR cc_start: 0.8537 (m-10) cc_final: 0.8307 (m-10) REVERT: O 83 ASP cc_start: 0.8210 (t0) cc_final: 0.7634 (t0) REVERT: N 48 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7169 (p0) REVERT: N 77 ARG cc_start: 0.8610 (mtp-110) cc_final: 0.8136 (ptm160) REVERT: N 122 MET cc_start: 0.8673 (mmm) cc_final: 0.8424 (mmm) REVERT: M 54 ASN cc_start: 0.7966 (m-40) cc_final: 0.7638 (m-40) REVERT: M 117 TYR cc_start: 0.8535 (m-10) cc_final: 0.8304 (m-10) REVERT: W 100 MET cc_start: 0.8489 (tpt) cc_final: 0.8130 (tpt) REVERT: V 122 MET cc_start: 0.8451 (tpt) cc_final: 0.7663 (tpp) REVERT: V 149 ASN cc_start: 0.7112 (m-40) cc_final: 0.6821 (m-40) REVERT: U 122 MET cc_start: 0.8200 (mmm) cc_final: 0.7699 (tpp) REVERT: T 100 MET cc_start: 0.8492 (tpt) cc_final: 0.8127 (tpt) REVERT: S 122 MET cc_start: 0.8428 (tpt) cc_final: 0.7605 (tpp) REVERT: S 149 ASN cc_start: 0.7115 (m-40) cc_final: 0.6824 (m-40) REVERT: L 146 ASP cc_start: 0.7348 (m-30) cc_final: 0.7114 (m-30) REVERT: K 146 ASP cc_start: 0.7515 (m-30) cc_final: 0.7032 (m-30) REVERT: J 126 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: H 146 ASP cc_start: 0.7521 (m-30) cc_final: 0.7040 (m-30) REVERT: G 126 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: B 281 TYR cc_start: 0.8126 (t80) cc_final: 0.7709 (t80) REVERT: B 528 ASP cc_start: 0.7830 (t0) cc_final: 0.7579 (t0) REVERT: C 674 ILE cc_start: 0.8788 (mm) cc_final: 0.8313 (mt) REVERT: D 745 ASP cc_start: 0.7896 (t0) cc_final: 0.7241 (t70) REVERT: E 281 TYR cc_start: 0.8131 (t80) cc_final: 0.7710 (t80) REVERT: E 528 ASP cc_start: 0.7830 (t0) cc_final: 0.7580 (t0) REVERT: F 674 ILE cc_start: 0.8793 (mm) cc_final: 0.8318 (mt) outliers start: 115 outliers final: 97 residues processed: 622 average time/residue: 0.5646 time to fit residues: 606.5422 Evaluate side-chains 618 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 517 time to evaluate : 5.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 48 ASP Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 118 PHE Chi-restraints excluded: chain O residue 118 PHE Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 48 ASP Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 118 PHE Chi-restraints excluded: chain X residue 9 SER Chi-restraints excluded: chain X residue 34 LEU Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 126 GLN Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 126 GLN Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 721 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 721 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 375 optimal weight: 1.9990 chunk 604 optimal weight: 2.9990 chunk 368 optimal weight: 4.9990 chunk 286 optimal weight: 0.0040 chunk 419 optimal weight: 7.9990 chunk 633 optimal weight: 0.8980 chunk 583 optimal weight: 8.9990 chunk 504 optimal weight: 0.9980 chunk 52 optimal weight: 0.0030 chunk 389 optimal weight: 6.9990 chunk 309 optimal weight: 0.0270 overall best weight: 0.3860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN R 46 GLN Q 54 ASN Q 111 ASN Q 129 ASN P 46 GLN ** P 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 GLN ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 ASN N 129 ASN M 46 GLN M 149 ASN D 537 GLN F 30 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 51054 Z= 0.121 Angle : 0.497 10.514 69756 Z= 0.265 Chirality : 0.044 0.176 8130 Planarity : 0.003 0.035 9036 Dihedral : 3.962 19.536 7122 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 1.90 % Allowed : 13.86 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.10), residues: 6378 helix: 0.70 (0.22), residues: 654 sheet: 0.45 (0.12), residues: 1884 loop : -1.55 (0.09), residues: 3840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP N 47 HIS 0.009 0.001 HIS N 52 PHE 0.018 0.001 PHE Q 107 TYR 0.012 0.001 TYR C 49 ARG 0.005 0.000 ARG Q 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12756 Ramachandran restraints generated. 6378 Oldfield, 0 Emsley, 6378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 585 time to evaluate : 5.681 Fit side-chains REVERT: A 745 ASP cc_start: 0.7770 (t0) cc_final: 0.7139 (t70) REVERT: R 83 ASP cc_start: 0.8086 (t0) cc_final: 0.7438 (t0) REVERT: Q 48 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7145 (p0) REVERT: Q 77 ARG cc_start: 0.8473 (mtp-110) cc_final: 0.8069 (ptm160) REVERT: Q 122 MET cc_start: 0.8458 (mmm) cc_final: 0.8249 (mmm) REVERT: P 54 ASN cc_start: 0.8006 (m-40) cc_final: 0.7683 (m-40) REVERT: P 117 TYR cc_start: 0.8419 (m-10) cc_final: 0.8145 (m-10) REVERT: O 77 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.7936 (ptm-80) REVERT: O 83 ASP cc_start: 0.8137 (t0) cc_final: 0.7491 (t0) REVERT: N 46 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7743 (mm110) REVERT: N 48 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6992 (p0) REVERT: N 77 ARG cc_start: 0.8474 (mtp-110) cc_final: 0.8071 (ptm160) REVERT: N 122 MET cc_start: 0.8463 (mmm) cc_final: 0.8250 (mmm) REVERT: M 54 ASN cc_start: 0.8004 (m-40) cc_final: 0.7683 (m-40) REVERT: M 117 TYR cc_start: 0.8418 (m-10) cc_final: 0.8142 (m-10) REVERT: X 122 MET cc_start: 0.8403 (mmm) cc_final: 0.7660 (tpp) REVERT: X 130 LEU cc_start: 0.8377 (tp) cc_final: 0.8006 (tt) REVERT: W 100 MET cc_start: 0.8468 (tpt) cc_final: 0.8114 (tpt) REVERT: V 122 MET cc_start: 0.8446 (tpt) cc_final: 0.7661 (tpp) REVERT: V 149 ASN cc_start: 0.7081 (m-40) cc_final: 0.6816 (m-40) REVERT: U 122 MET cc_start: 0.7962 (mmm) cc_final: 0.7533 (tpp) REVERT: U 130 LEU cc_start: 0.8374 (tp) cc_final: 0.8019 (tt) REVERT: T 100 MET cc_start: 0.8471 (tpt) cc_final: 0.8113 (tpt) REVERT: S 122 MET cc_start: 0.8448 (tpt) cc_final: 0.7669 (tpp) REVERT: S 149 ASN cc_start: 0.7084 (m-40) cc_final: 0.6821 (m-40) REVERT: L 146 ASP cc_start: 0.7196 (m-30) cc_final: 0.6920 (m-30) REVERT: K 146 ASP cc_start: 0.7423 (m-30) cc_final: 0.6949 (m-30) REVERT: J 26 ASP cc_start: 0.8006 (t0) cc_final: 0.7745 (t0) REVERT: H 146 ASP cc_start: 0.7428 (m-30) cc_final: 0.6955 (m-30) REVERT: G 26 ASP cc_start: 0.8012 (t0) cc_final: 0.7751 (t0) REVERT: B 281 TYR cc_start: 0.8111 (t80) cc_final: 0.7733 (t80) REVERT: C 459 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8620 (t) REVERT: C 674 ILE cc_start: 0.8684 (mm) cc_final: 0.8259 (mm) REVERT: C 721 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8393 (mt-10) REVERT: D 745 ASP cc_start: 0.7768 (t0) cc_final: 0.7134 (t70) REVERT: E 281 TYR cc_start: 0.8116 (t80) cc_final: 0.7733 (t80) REVERT: F 459 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8624 (t) REVERT: F 674 ILE cc_start: 0.8687 (mm) cc_final: 0.8260 (mm) REVERT: F 721 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8390 (mt-10) outliers start: 101 outliers final: 83 residues processed: 665 average time/residue: 0.5713 time to fit residues: 652.7194 Evaluate side-chains 634 residues out of total 5556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 545 time to evaluate : 5.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain Q residue 48 ASP Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 118 PHE Chi-restraints excluded: chain O residue 118 PHE Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain M residue 48 ASP Chi-restraints excluded: chain M residue 118 PHE Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 126 GLN Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 721 GLU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 721 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 400 optimal weight: 3.9990 chunk 537 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 465 optimal weight: 9.9990 chunk 74 optimal weight: 0.4980 chunk 140 optimal weight: 4.9990 chunk 505 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 518 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 537 GLN Q 111 ASN P 149 ASN O 5 GLN O 149 ASN N 54 ASN N 111 ASN M 149 ASN L 52 HIS B 414 GLN C 414 GLN D 30 GLN D 414 GLN E 414 GLN F 30 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.079140 restraints weight = 89902.554| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.34 r_work: 0.2827 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 51054 Z= 0.345 Angle : 0.628 10.696 69756 Z= 0.335 Chirality : 0.049 0.250 8130 Planarity : 0.004 0.033 9036 Dihedral : 4.609 28.326 7122 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.85 % Favored : 93.05 % Rotamer: Outliers : 2.15 % Allowed : 14.20 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.10), residues: 6378 helix: 0.47 (0.21), residues: 654 sheet: 0.28 (0.12), residues: 1992 loop : -1.74 (0.09), residues: 3732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 627 HIS 0.007 0.001 HIS D 536 PHE 0.021 0.002 PHE Q 107 TYR 0.020 0.002 TYR A 588 ARG 0.009 0.001 ARG R 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12005.34 seconds wall clock time: 214 minutes 2.88 seconds (12842.88 seconds total)