Starting phenix.real_space_refine on Thu Jan 16 03:39:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5lmn_4073/01_2025/5lmn_4073_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5lmn_4073/01_2025/5lmn_4073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5lmn_4073/01_2025/5lmn_4073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5lmn_4073/01_2025/5lmn_4073.map" model { file = "/net/cci-nas-00/data/ceres_data/5lmn_4073/01_2025/5lmn_4073_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5lmn_4073/01_2025/5lmn_4073_neut.cif" } resolution = 3.55 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= -0.000 sd= 0.029 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1532 5.49 5 Mg 127 5.21 5 S 60 5.16 5 C 27936 2.51 5 N 10188 2.21 5 O 14304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 54149 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 32527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1514, 32527 Inner-chain residues flagged as termini: ['pdbres=" G A 567 "'] Classifications: {'RNA': 1514} Modifications used: {'5*END': 2, 'rna2p_pur': 106, 'rna2p_pyr': 79, 'rna3p_pur': 749, 'rna3p_pyr': 579} Link IDs: {'rna2p': 185, 'rna3p': 1328} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1900 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 11, 'TRANS': 222} Chain: "C" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "D" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "E" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1146 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "F" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "G" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1257 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "H" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "I" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 999 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 792 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 892 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "L" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 970 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "M" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 933 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "N" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "O" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "P" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 700 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "Q" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 823 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "R" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 598 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "S" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 647 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "T" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 763 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "V" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 208 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "W" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 570 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "X" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1356 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 160} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 439 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 2} Link IDs: {'rna2p': 5, 'rna3p': 14} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Unusual residues: {' MG': 126} Classifications: {'undetermined': 126} Link IDs: {None: 125} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36098 SG CYS D 9 85.820 103.529 147.785 1.00 25.92 S ATOM 36241 SG CYS D 26 83.109 105.000 147.741 1.00 42.34 S ATOM 36281 SG CYS D 31 84.953 106.919 146.909 1.00 57.10 S ATOM 46881 SG CYS N 24 148.205 114.068 137.058 1.00 45.04 S ATOM 46905 SG CYS N 27 146.059 110.867 136.254 1.00 46.39 S ATOM 47012 SG CYS N 40 147.821 113.126 133.568 1.00 43.14 S ATOM 47037 SG CYS N 43 144.994 114.586 135.557 1.00 40.46 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN N1602 " occ=0.92 Time building chain proxies: 21.42, per 1000 atoms: 0.40 Number of scatterers: 54149 At special positions: 0 Unit cell: (225.12, 179.56, 209.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 60 16.00 P 1532 15.00 Mg 127 11.99 O 14304 8.00 N 10188 7.00 C 27936 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: 9.25 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 300 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 9 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 31 " pdb=" ZN N1602 " pdb="ZN ZN N1602 " - pdb=" SG CYS N 40 " pdb="ZN ZN N1602 " - pdb=" SG CYS N 43 " pdb="ZN ZN N1602 " - pdb=" SG CYS N 24 " pdb="ZN ZN N1602 " - pdb=" SG CYS N 27 " Number of angles added : 6 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4844 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 29 sheets defined 40.5% alpha, 17.8% beta 508 base pairs and 868 stacking pairs defined. Time for finding SS restraints: 19.78 Creating SS restraints... Processing helix chain 'B' and resid 27 through 30 removed outlier: 3.825A pdb=" N ARG B 30 " --> pdb=" O LYS B 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 43 through 63 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.637A pdb=" N ARG B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 122 removed outlier: 3.535A pdb=" N GLN B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 removed outlier: 4.552A pdb=" N LYS B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 180 Processing helix chain 'B' and resid 207 through 227 removed outlier: 3.594A pdb=" N ILE B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.661A pdb=" N VAL B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 240' Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.508A pdb=" N LEU C 32 " --> pdb=" O GLN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.845A pdb=" N VAL C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 108 through 111 removed outlier: 3.674A pdb=" N LEU C 111 " --> pdb=" O ASN C 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 111' Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 145 removed outlier: 3.507A pdb=" N GLY C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.643A pdb=" N ALA C 160 " --> pdb=" O ILE C 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 15 Processing helix chain 'D' and resid 52 through 69 Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 88 through 100 removed outlier: 3.544A pdb=" N ARG D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 149 through 154 removed outlier: 4.432A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 166 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.711A pdb=" N VAL D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 65 Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.804A pdb=" N LEU E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 142 Processing helix chain 'E' and resid 144 through 152 Processing helix chain 'F' and resid 17 through 33 Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 71 through 82 removed outlier: 4.241A pdb=" N ARG F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 53 Processing helix chain 'G' and resid 57 through 70 Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 132 through 147 Processing helix chain 'G' and resid 148 through 154 removed outlier: 4.249A pdb=" N HIS G 153 " --> pdb=" O ALA G 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 19 Processing helix chain 'H' and resid 29 through 43 Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.537A pdb=" N ILE H 100 " --> pdb=" O VAL H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 107 removed outlier: 3.686A pdb=" N ARG H 105 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'I' and resid 33 through 37 Processing helix chain 'I' and resid 42 through 46 Processing helix chain 'I' and resid 47 through 54 removed outlier: 3.645A pdb=" N ARG I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 89 Processing helix chain 'I' and resid 90 through 93 removed outlier: 3.594A pdb=" N ARG I 93 " --> pdb=" O PRO I 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 90 through 93' Processing helix chain 'J' and resid 12 through 29 removed outlier: 3.604A pdb=" N ALA J 18 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 49 Processing helix chain 'K' and resid 53 through 56 Processing helix chain 'K' and resid 57 through 74 Processing helix chain 'K' and resid 89 through 101 removed outlier: 4.571A pdb=" N GLN K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 14 Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.942A pdb=" N TYR M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.521A pdb=" N VAL M 54 " --> pdb=" O GLU M 50 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG M 55 " --> pdb=" O ALA M 51 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.831A pdb=" N ILE M 84 " --> pdb=" O ARG M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 95 Processing helix chain 'M' and resid 107 through 112 Processing helix chain 'N' and resid 3 through 7 Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 Processing helix chain 'O' and resid 50 through 74 removed outlier: 3.529A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 52 through 62 removed outlier: 3.638A pdb=" N ALA P 56 " --> pdb=" O ASP P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 77 Processing helix chain 'Q' and resid 81 through 95 removed outlier: 3.915A pdb=" N VAL Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR Q 95 " --> pdb=" O ARG Q 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 26 removed outlier: 3.618A pdb=" N LEU R 26 " --> pdb=" O VAL R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 57 Processing helix chain 'R' and resid 59 through 77 Processing helix chain 'S' and resid 12 through 25 removed outlier: 4.414A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 45 Processing helix chain 'S' and resid 71 through 75 Processing helix chain 'T' and resid 13 through 47 removed outlier: 3.591A pdb=" N GLU T 46 " --> pdb=" O GLN T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 69 removed outlier: 3.594A pdb=" N GLY T 69 " --> pdb=" O LYS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 94 Processing helix chain 'V' and resid 8 through 15 Processing helix chain 'W' and resid 37 through 43 Processing helix chain 'X' and resid 31 through 42 Processing helix chain 'X' and resid 61 through 79 Processing helix chain 'X' and resid 95 through 113 Processing helix chain 'X' and resid 128 through 144 removed outlier: 3.542A pdb=" N LEU X 132 " --> pdb=" O ALA X 128 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 93 removed outlier: 7.969A pdb=" N VAL B 93 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N PHE B 70 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL B 184 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 60 removed outlier: 3.963A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 63 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASN C 102 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL C 68 " --> pdb=" O GLN C 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 171 Processing sheet with id=AA5, first strand: chain 'D' and resid 126 through 128 removed outlier: 3.663A pdb=" N ASP D 144 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 7 through 20 removed outlier: 5.208A pdb=" N GLU E 8 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY E 35 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N MET E 10 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL E 33 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E 16 " --> pdb=" O ARG E 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 80 through 84 Processing sheet with id=AA8, first strand: chain 'F' and resid 36 through 37 removed outlier: 3.684A pdb=" N GLY F 44 " --> pdb=" O PHE F 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 36 through 37 Processing sheet with id=AB1, first strand: chain 'F' and resid 98 through 99 removed outlier: 3.767A pdb=" N ALA F 99 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE R 29 " --> pdb=" O ALA F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 73 through 79 Processing sheet with id=AB3, first strand: chain 'H' and resid 23 through 27 removed outlier: 3.761A pdb=" N GLY H 47 " --> pdb=" O TYR H 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AB5, first strand: chain 'H' and resid 83 through 85 Processing sheet with id=AB6, first strand: chain 'H' and resid 83 through 85 removed outlier: 4.917A pdb=" N LEU H 133 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N SER H 113 " --> pdb=" O LEU H 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 6 removed outlier: 5.963A pdb=" N THR I 27 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL I 65 " --> pdb=" O THR I 27 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 38 through 43 removed outlier: 4.058A pdb=" N ASN J 69 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR J 42 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N THR J 67 " --> pdb=" O THR J 42 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 47 through 50 removed outlier: 3.890A pdb=" N VAL J 49 " --> pdb=" O GLU J 61 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 39 through 43 removed outlier: 6.061A pdb=" N ALA K 19 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG K 85 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE K 21 " --> pdb=" O ARG K 85 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL K 80 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE K 108 " --> pdb=" O VAL K 80 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL K 82 " --> pdb=" O ILE K 108 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP K 110 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL K 84 " --> pdb=" O ASP K 110 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 82 through 84 removed outlier: 6.478A pdb=" N LYS L 57 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL L 40 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL L 55 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR L 42 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG L 53 " --> pdb=" O THR L 42 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR L 98 " --> pdb=" O THR L 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 34 through 35 Processing sheet with id=AC5, first strand: chain 'P' and resid 37 through 39 Processing sheet with id=AC6, first strand: chain 'Q' and resid 5 through 15 removed outlier: 6.950A pdb=" N GLY Q 8 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLU Q 24 " --> pdb=" O GLY Q 8 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL Q 10 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU Q 22 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS Q 14 " --> pdb=" O THR Q 18 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR Q 18 " --> pdb=" O LYS Q 14 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG Q 38 " --> pdb=" O ARG Q 25 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE Q 71 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU Q 76 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL Q 56 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 31 through 33 Processing sheet with id=AC8, first strand: chain 'W' and resid 10 through 17 removed outlier: 5.335A pdb=" N VAL W 13 " --> pdb=" O LYS W 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS W 25 " --> pdb=" O VAL W 13 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR W 21 " --> pdb=" O LEU W 17 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE W 32 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N GLY W 65 " --> pdb=" O GLU W 31 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU W 33 " --> pdb=" O GLY W 65 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE W 67 " --> pdb=" O LEU W 33 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR W 35 " --> pdb=" O ILE W 67 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N TYR W 69 " --> pdb=" O TYR W 35 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL W 54 " --> pdb=" O VAL W 68 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 27 through 30 removed outlier: 3.720A pdb=" N GLY X 27 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ALA X 57 " --> pdb=" O GLN X 15 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARG X 17 " --> pdb=" O ALA X 57 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE X 59 " --> pdb=" O ARG X 17 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL X 19 " --> pdb=" O ILE X 59 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG X 58 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU X 47 " --> pdb=" O ARG X 58 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N MET X 60 " --> pdb=" O LEU X 45 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU X 45 " --> pdb=" O MET X 60 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 85 through 87 Processing sheet with id=AD2, first strand: chain 'X' and resid 120 through 121 946 hydrogen bonds defined for protein. 2703 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1353 hydrogen bonds 2290 hydrogen bond angles 0 basepair planarities 508 basepair parallelities 868 stacking parallelities Total time for adding SS restraints: 44.52 Time building geometry restraints manager: 11.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6986 1.33 - 1.45: 24769 1.45 - 1.58: 23432 1.58 - 1.71: 2991 1.71 - 1.83: 107 Bond restraints: 58285 Sorted by residual: bond pdb=" O3' C A1459 " pdb=" P A A1460 " ideal model delta sigma weight residual 1.607 1.505 0.102 1.50e-02 4.44e+03 4.66e+01 bond pdb=" O3' G A1458 " pdb=" P C A1459 " ideal model delta sigma weight residual 1.607 1.697 -0.090 1.50e-02 4.44e+03 3.61e+01 bond pdb=" O3' C A 999 " pdb=" P U A1000 " ideal model delta sigma weight residual 1.607 1.539 0.068 1.50e-02 4.44e+03 2.04e+01 bond pdb=" O3' A A 559 " pdb=" P U A 560 " ideal model delta sigma weight residual 1.607 1.671 -0.064 1.50e-02 4.44e+03 1.80e+01 bond pdb=" O3' G A 79 " pdb=" P G A 80 " ideal model delta sigma weight residual 1.607 1.545 0.062 1.50e-02 4.44e+03 1.71e+01 ... (remaining 58280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.31: 86229 10.31 - 20.63: 39 20.63 - 30.94: 1 30.94 - 41.26: 0 41.26 - 51.57: 2 Bond angle restraints: 86271 Sorted by residual: angle pdb=" O3' G A 93 " pdb=" P U A 96 " pdb=" O5' U A 96 " ideal model delta sigma weight residual 104.00 53.24 50.76 1.50e+00 4.44e-01 1.15e+03 angle pdb=" O3' G A 93 " pdb=" P U A 96 " pdb=" OP1 U A 96 " ideal model delta sigma weight residual 108.00 56.43 51.57 3.00e+00 1.11e-01 2.95e+02 angle pdb=" N ILE C 14 " pdb=" CA ILE C 14 " pdb=" C ILE C 14 " ideal model delta sigma weight residual 111.62 122.82 -11.20 7.90e-01 1.60e+00 2.01e+02 angle pdb=" C4' A A1001 " pdb=" C3' A A1001 " pdb=" O3' A A1001 " ideal model delta sigma weight residual 113.00 92.24 20.76 1.50e+00 4.44e-01 1.91e+02 angle pdb=" O3' G A 266 " pdb=" C3' G A 266 " pdb=" C2' G A 266 " ideal model delta sigma weight residual 109.50 128.07 -18.57 1.50e+00 4.44e-01 1.53e+02 ... (remaining 86266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 32083 35.99 - 71.97: 4932 71.97 - 107.96: 590 107.96 - 143.95: 22 143.95 - 179.93: 45 Dihedral angle restraints: 37672 sinusoidal: 30137 harmonic: 7535 Sorted by residual: dihedral pdb=" C5' C A1145 " pdb=" C4' C A1145 " pdb=" C3' C A1145 " pdb=" O3' C A1145 " ideal model delta sinusoidal sigma weight residual 147.00 73.42 73.58 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" C5' G A1504 " pdb=" C4' G A1504 " pdb=" C3' G A1504 " pdb=" O3' G A1504 " ideal model delta sinusoidal sigma weight residual 147.00 73.47 73.53 1 8.00e+00 1.56e-02 1.07e+02 dihedral pdb=" C5' C A 840 " pdb=" C4' C A 840 " pdb=" C3' C A 840 " pdb=" O3' C A 840 " ideal model delta sinusoidal sigma weight residual 147.00 76.99 70.01 1 8.00e+00 1.56e-02 9.87e+01 ... (remaining 37669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.236: 10301 0.236 - 0.471: 473 0.471 - 0.707: 22 0.707 - 0.943: 10 0.943 - 1.178: 2 Chirality restraints: 10808 Sorted by residual: chirality pdb=" C3' G A 115 " pdb=" C4' G A 115 " pdb=" O3' G A 115 " pdb=" C2' G A 115 " both_signs ideal model delta sigma weight residual False -2.74 -1.57 -1.18 2.00e-01 2.50e+01 3.47e+01 chirality pdb=" C3' U A1498 " pdb=" C4' U A1498 " pdb=" O3' U A1498 " pdb=" C2' U A1498 " both_signs ideal model delta sigma weight residual False -2.74 -1.69 -1.06 2.00e-01 2.50e+01 2.80e+01 chirality pdb=" C3' G A 181 " pdb=" C4' G A 181 " pdb=" O3' G A 181 " pdb=" C2' G A 181 " both_signs ideal model delta sigma weight residual False -2.74 -1.86 -0.89 2.00e-01 2.50e+01 1.98e+01 ... (remaining 10805 not shown) Planarity restraints: 5246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1458 " 0.051 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" N9 G A1458 " 0.006 2.00e-02 2.50e+03 pdb=" C8 G A1458 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A1458 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A1458 " -0.052 2.00e-02 2.50e+03 pdb=" C6 G A1458 " -0.093 2.00e-02 2.50e+03 pdb=" O6 G A1458 " 0.131 2.00e-02 2.50e+03 pdb=" N1 G A1458 " -0.022 2.00e-02 2.50e+03 pdb=" C2 G A1458 " -0.080 2.00e-02 2.50e+03 pdb=" N2 G A1458 " 0.075 2.00e-02 2.50e+03 pdb=" N3 G A1458 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A1458 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 76 " 0.044 2.00e-02 2.50e+03 5.59e-02 7.04e+01 pdb=" N1 C A 76 " -0.009 2.00e-02 2.50e+03 pdb=" C2 C A 76 " -0.118 2.00e-02 2.50e+03 pdb=" O2 C A 76 " 0.070 2.00e-02 2.50e+03 pdb=" N3 C A 76 " -0.015 2.00e-02 2.50e+03 pdb=" C4 C A 76 " -0.044 2.00e-02 2.50e+03 pdb=" N4 C A 76 " 0.071 2.00e-02 2.50e+03 pdb=" C5 C A 76 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C A 76 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 70 " -0.011 2.00e-02 2.50e+03 4.82e-02 6.98e+01 pdb=" N9 G A 70 " -0.007 2.00e-02 2.50e+03 pdb=" C8 G A 70 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G A 70 " 0.017 2.00e-02 2.50e+03 pdb=" C5 G A 70 " 0.014 2.00e-02 2.50e+03 pdb=" C6 G A 70 " -0.103 2.00e-02 2.50e+03 pdb=" O6 G A 70 " 0.064 2.00e-02 2.50e+03 pdb=" N1 G A 70 " -0.023 2.00e-02 2.50e+03 pdb=" C2 G A 70 " -0.070 2.00e-02 2.50e+03 pdb=" N2 G A 70 " 0.075 2.00e-02 2.50e+03 pdb=" N3 G A 70 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 70 " 0.038 2.00e-02 2.50e+03 ... (remaining 5243 not shown) Histogram of nonbonded interaction distances: 0.93 - 1.72: 21 1.72 - 2.52: 302 2.52 - 3.31: 62438 3.31 - 4.10: 188045 4.10 - 4.90: 266197 Warning: very small nonbonded interaction distances. Nonbonded interactions: 517003 Sorted by model distance: nonbonded pdb=" CD1 LEU B 10 " pdb=" SD MET B 48 " model vdw 0.925 3.820 nonbonded pdb=" CG ARG N 23 " pdb=" O ARG N 29 " model vdw 1.162 3.440 nonbonded pdb=" O LYS J 57 " pdb=" NH2 ARG J 60 " model vdw 1.302 3.120 nonbonded pdb=" NZ LYS J 57 " pdb=" NH1 ARG J 60 " model vdw 1.414 3.200 nonbonded pdb=" CD1 LEU B 10 " pdb=" CG MET B 48 " model vdw 1.419 3.860 ... (remaining 516998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.92 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.030 Extract box with map and model: 1.490 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 129.880 Find NCS groups from input model: 0.510 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 58285 Z= 0.452 Angle : 1.421 51.570 86271 Z= 0.947 Chirality : 0.116 1.178 10808 Planarity : 0.010 0.184 5246 Dihedral : 26.546 179.933 32828 Min Nonbonded Distance : 0.925 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 2.83 % Allowed : 10.43 % Favored : 86.74 % Rotamer: Outliers : 21.59 % Allowed : 19.32 % Favored : 59.09 % Cbeta Deviations : 1.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.30 (0.15), residues: 2579 helix: 0.34 (0.14), residues: 1004 sheet: -2.10 (0.22), residues: 423 loop : -3.10 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP P 59 HIS 0.014 0.002 HIS D 43 PHE 0.029 0.003 PHE O 15 TYR 0.028 0.003 TYR D 4 ARG 0.026 0.002 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1462 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 474 poor density : 988 time to evaluate : 2.647 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ASN cc_start: 0.7196 (m-40) cc_final: 0.6770 (m-40) REVERT: B 44 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7550 (tp) REVERT: B 75 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.7923 (ttmt) REVERT: B 83 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7337 (ttt) REVERT: B 90 MET cc_start: 0.8514 (mmt) cc_final: 0.8287 (mmp) REVERT: B 101 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8654 (mtt) REVERT: B 110 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8500 (mm-40) REVERT: B 126 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6694 (tm-30) REVERT: B 146 GLN cc_start: 0.8677 (tp-100) cc_final: 0.8463 (tp40) REVERT: B 156 LYS cc_start: 0.7592 (tttt) cc_final: 0.7387 (tttp) REVERT: B 178 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7728 (mmt180) REVERT: B 184 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8803 (t) REVERT: B 222 ILE cc_start: 0.8519 (mt) cc_final: 0.8269 (tp) REVERT: C 3 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8127 (p0) REVERT: C 45 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8591 (tppt) REVERT: C 70 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8272 (p) REVERT: C 72 LYS cc_start: 0.8599 (mmpt) cc_final: 0.8002 (ptpp) REVERT: C 94 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8262 (mt) REVERT: C 97 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8183 (mtpp) REVERT: C 104 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7943 (tm-30) REVERT: C 107 GLN cc_start: 0.7622 (mp10) cc_final: 0.7106 (mm-40) REVERT: C 136 GLN cc_start: 0.8705 (mt0) cc_final: 0.8365 (mt0) REVERT: C 181 ASN cc_start: 0.9468 (t0) cc_final: 0.9231 (t0) REVERT: C 183 ASP cc_start: 0.8712 (t0) cc_final: 0.8403 (t0) REVERT: C 190 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7951 (ttp-170) REVERT: C 204 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8946 (pp) REVERT: D 26 CYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9160 (t) REVERT: D 35 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6474 (ptm160) REVERT: D 42 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: D 49 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7765 (mtm180) REVERT: D 59 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8647 (tpp-160) REVERT: D 61 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8696 (ttpp) REVERT: D 64 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8969 (tp) REVERT: D 66 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8321 (mmt180) REVERT: D 67 ILE cc_start: 0.9300 (mt) cc_final: 0.9028 (mt) REVERT: D 119 GLN cc_start: 0.8904 (tm-30) cc_final: 0.7988 (tm-30) REVERT: D 126 ILE cc_start: 0.9201 (mm) cc_final: 0.8836 (mm) REVERT: D 131 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8588 (ttp-110) REVERT: D 132 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7732 (ttp-110) REVERT: D 157 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8851 (tt) REVERT: D 182 LYS cc_start: 0.8154 (mttt) cc_final: 0.7902 (mtpt) REVERT: D 190 ASP cc_start: 0.8195 (t70) cc_final: 0.7951 (m-30) REVERT: E 65 ASN cc_start: 0.8759 (t0) cc_final: 0.8497 (t0) REVERT: E 71 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7844 (tt) REVERT: E 147 ASP cc_start: 0.8759 (t70) cc_final: 0.8543 (t0) REVERT: E 149 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: F 5 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8622 (mt-10) REVERT: F 7 ASN cc_start: 0.8276 (m-40) cc_final: 0.7845 (m-40) REVERT: F 11 ASN cc_start: 0.8714 (t0) cc_final: 0.8413 (t0) REVERT: F 15 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8526 (p0) REVERT: F 36 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7638 (ttp80) REVERT: F 38 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7692 (mt-10) REVERT: F 64 GLN cc_start: 0.8492 (tt0) cc_final: 0.8242 (tt0) REVERT: F 65 VAL cc_start: 0.9531 (OUTLIER) cc_final: 0.9331 (p) REVERT: F 66 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7733 (mt-10) REVERT: F 74 ASP cc_start: 0.8746 (t0) cc_final: 0.7919 (t0) REVERT: F 86 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8058 (mtt90) REVERT: F 95 GLU cc_start: 0.9063 (tt0) cc_final: 0.8476 (pm20) REVERT: G 13 GLN cc_start: 0.9273 (tm-30) cc_final: 0.8996 (tm-30) REVERT: G 94 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7738 (ttp80) REVERT: G 95 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8196 (tpt-90) REVERT: G 106 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8367 (mm-40) REVERT: G 110 GLN cc_start: 0.9038 (mm110) cc_final: 0.8726 (mm-40) REVERT: G 125 MET cc_start: 0.7409 (mtm) cc_final: 0.7120 (mtm) REVERT: G 126 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: G 139 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: G 140 ASP cc_start: 0.7734 (m-30) cc_final: 0.7279 (m-30) REVERT: H 18 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7859 (mpt180) REVERT: H 37 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7720 (tmm-80) REVERT: H 68 ARG cc_start: 0.7264 (tpt-90) cc_final: 0.7062 (tpt-90) REVERT: H 86 ILE cc_start: 0.9096 (mt) cc_final: 0.8594 (mt) REVERT: H 105 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7611 (tpm170) REVERT: H 112 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8972 (mp) REVERT: H 127 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8993 (mp) REVERT: H 132 GLU cc_start: 0.8757 (tt0) cc_final: 0.8551 (tt0) REVERT: I 4 TYR cc_start: 0.7807 (m-80) cc_final: 0.7397 (m-80) REVERT: I 5 TYR cc_start: 0.7099 (t80) cc_final: 0.6876 (t80) REVERT: I 31 GLN cc_start: 0.8931 (mt0) cc_final: 0.8695 (mt0) REVERT: I 34 ASN cc_start: 0.9151 (m-40) cc_final: 0.8751 (t0) REVERT: I 38 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: I 56 LEU cc_start: 0.6333 (mt) cc_final: 0.6038 (mp) REVERT: I 62 TYR cc_start: 0.8347 (t80) cc_final: 0.7865 (t80) REVERT: I 70 LYS cc_start: 0.8598 (mmtt) cc_final: 0.7902 (mmtt) REVERT: I 73 GLN cc_start: 0.8316 (mt0) cc_final: 0.7926 (mt0) REVERT: I 74 ILE cc_start: 0.9087 (mt) cc_final: 0.8810 (mt) REVERT: I 89 ASN cc_start: 0.7933 (t0) cc_final: 0.7632 (t0) REVERT: I 95 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8471 (mtpt) REVERT: I 114 TYR cc_start: 0.8930 (p90) cc_final: 0.8640 (p90) REVERT: I 118 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7580 (tttt) REVERT: I 125 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7300 (p90) REVERT: J 5 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7838 (ttt180) REVERT: J 7 LYS cc_start: 0.8226 (tttp) cc_final: 0.7941 (tttt) REVERT: J 42 THR cc_start: 0.9423 (m) cc_final: 0.9196 (p) REVERT: J 43 ARG cc_start: 0.8906 (mmt90) cc_final: 0.8627 (mtt-85) REVERT: J 55 LYS cc_start: 0.8726 (pttt) cc_final: 0.8412 (pttt) REVERT: J 67 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.8850 (t) REVERT: J 69 ASN cc_start: 0.8759 (m-40) cc_final: 0.8497 (m-40) REVERT: J 82 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8574 (tt) REVERT: J 99 LYS cc_start: 0.7624 (mmtt) cc_final: 0.7346 (mmmt) REVERT: K 24 SER cc_start: 0.9327 (t) cc_final: 0.8947 (p) REVERT: K 30 VAL cc_start: 0.9545 (t) cc_final: 0.9329 (p) REVERT: K 36 ASP cc_start: 0.8820 (t70) cc_final: 0.8379 (m-30) REVERT: K 54 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8655 (mtt180) REVERT: K 71 LYS cc_start: 0.8593 (mttt) cc_final: 0.8299 (mttt) REVERT: K 84 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8806 (p) REVERT: K 93 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7900 (tp40) REVERT: K 117 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8550 (t0) REVERT: L 42 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8222 (p) REVERT: L 59 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7865 (ptm-80) REVERT: L 64 TYR cc_start: 0.7692 (m-80) cc_final: 0.7474 (m-10) REVERT: L 65 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: L 69 TYR cc_start: 0.9061 (t80) cc_final: 0.8729 (t80) REVERT: L 70 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9118 (mp) REVERT: L 113 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.7908 (mmm-85) REVERT: M 27 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8680 (ttmt) REVERT: M 52 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8256 (mt-10) REVERT: M 71 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7197 (mtp-110) REVERT: M 83 ASP cc_start: 0.9035 (m-30) cc_final: 0.8380 (p0) REVERT: N 9 LYS cc_start: 0.7769 (tmtt) cc_final: 0.7516 (tmtt) REVERT: N 29 ARG cc_start: 0.7781 (ttt-90) cc_final: 0.7546 (ttt-90) REVERT: N 31 ARG cc_start: 0.8365 (tpt-90) cc_final: 0.7674 (tpp80) REVERT: N 32 SER cc_start: 0.9036 (t) cc_final: 0.8617 (t) REVERT: O 8 LYS cc_start: 0.8966 (tttt) cc_final: 0.8662 (mttt) REVERT: O 13 GLN cc_start: 0.9059 (mp10) cc_final: 0.8808 (mp10) REVERT: O 14 GLU cc_start: 0.8860 (tp30) cc_final: 0.8597 (tp30) REVERT: O 22 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8681 (t) REVERT: O 84 LYS cc_start: 0.8766 (tttt) cc_final: 0.8366 (mtpt) REVERT: P 44 THR cc_start: 0.9228 (p) cc_final: 0.8780 (p) REVERT: P 49 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8698 (tp) REVERT: P 50 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8713 (tttp) REVERT: P 69 THR cc_start: 0.8995 (m) cc_final: 0.8786 (m) REVERT: Q 16 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: Q 31 LEU cc_start: 0.9277 (tp) cc_final: 0.9008 (tp) REVERT: Q 34 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8783 (tttp) REVERT: Q 46 ASP cc_start: 0.9075 (t0) cc_final: 0.8586 (t0) REVERT: Q 49 GLU cc_start: 0.8993 (tt0) cc_final: 0.8362 (tt0) REVERT: Q 50 LYS cc_start: 0.8221 (tttt) cc_final: 0.7702 (tptm) REVERT: Q 62 SER cc_start: 0.9317 (m) cc_final: 0.8717 (t) REVERT: Q 68 ARG cc_start: 0.9000 (ptm-80) cc_final: 0.8682 (ptm-80) REVERT: Q 81 ARG cc_start: 0.9179 (ptm160) cc_final: 0.8807 (ptm160) REVERT: Q 87 LYS cc_start: 0.8813 (mttt) cc_final: 0.8515 (mtmm) REVERT: Q 89 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8725 (mt) REVERT: Q 93 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7243 (tp40) REVERT: R 28 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6560 (mp0) REVERT: R 40 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8725 (mt) REVERT: R 54 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8313 (ptt180) REVERT: R 55 ARG cc_start: 0.8712 (mmm160) cc_final: 0.7779 (mpt180) REVERT: R 76 LEU cc_start: 0.9028 (mt) cc_final: 0.8809 (mt) REVERT: R 83 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7720 (tp30) REVERT: S 5 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7169 (mt) REVERT: S 15 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8535 (tt) REVERT: S 21 GLU cc_start: 0.8517 (tt0) cc_final: 0.8229 (tt0) REVERT: S 31 ILE cc_start: 0.7987 (mm) cc_final: 0.7303 (mm) REVERT: S 32 LYS cc_start: 0.8598 (mtpm) cc_final: 0.8271 (mmpt) REVERT: S 41 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8473 (p) REVERT: S 43 GLU cc_start: 0.8174 (pm20) cc_final: 0.7827 (pm20) REVERT: S 44 MET cc_start: 0.8860 (mtt) cc_final: 0.8497 (mtp) REVERT: S 60 VAL cc_start: 0.8455 (t) cc_final: 0.8246 (t) REVERT: S 62 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8440 (mp) REVERT: S 70 LYS cc_start: 0.8081 (mptt) cc_final: 0.7479 (mmtm) REVERT: S 71 LEU cc_start: 0.8063 (tt) cc_final: 0.7850 (tt) REVERT: S 78 ARG cc_start: 0.7973 (ptp-110) cc_final: 0.7634 (mtm-85) REVERT: T 8 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.5962 (ppt90) REVERT: T 22 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8118 (mtt180) REVERT: T 23 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8775 (ttp80) REVERT: T 27 LYS cc_start: 0.8674 (tptt) cc_final: 0.8424 (tttp) REVERT: T 31 SER cc_start: 0.9123 (t) cc_final: 0.8872 (p) REVERT: T 42 GLN cc_start: 0.8993 (mm110) cc_final: 0.8687 (tp40) REVERT: T 46 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: T 58 LYS cc_start: 0.8452 (mttt) cc_final: 0.8176 (tppt) REVERT: T 64 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8203 (m-30) REVERT: V 5 ASP cc_start: 0.6908 (t0) cc_final: 0.6601 (t0) REVERT: W 25 LYS cc_start: 0.7527 (tptm) cc_final: 0.7117 (ptpt) REVERT: W 37 SER cc_start: 0.8862 (t) cc_final: 0.8606 (t) REVERT: W 47 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8423 (mm) REVERT: W 68 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8459 (m) REVERT: X 35 LEU cc_start: 0.5520 (OUTLIER) cc_final: 0.5190 (tp) REVERT: X 41 MET cc_start: 0.4000 (mmm) cc_final: 0.3437 (ttt) REVERT: X 62 TYR cc_start: 0.8083 (t80) cc_final: 0.7496 (t80) REVERT: X 69 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8712 (tt0) REVERT: X 78 LYS cc_start: 0.7528 (ptmm) cc_final: 0.7299 (pttp) REVERT: X 123 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7587 (mtp-110) REVERT: X 152 MET cc_start: 0.7632 (mmm) cc_final: 0.7344 (mmm) REVERT: X 155 GLU cc_start: 0.8915 (tt0) cc_final: 0.8519 (tm-30) REVERT: X 168 VAL cc_start: 0.5307 (OUTLIER) cc_final: 0.5084 (p) outliers start: 474 outliers final: 124 residues processed: 1233 average time/residue: 0.6528 time to fit residues: 1239.5942 Evaluate side-chains 989 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 781 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 14 ARG Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 86 ARG Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 GLN Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 124 GLN Chi-restraints excluded: chain I residue 125 TYR Chi-restraints excluded: chain J residue 5 ARG Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 34 ARG Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 ARG Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 ARG Chi-restraints excluded: chain L residue 65 GLU Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 89 ARG Chi-restraints excluded: chain L residue 113 ARG Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 21 TYR Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 65 ARG Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 6 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 50 LYS Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 16 GLN Chi-restraints excluded: chain Q residue 34 LYS Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain Q residue 63 ARG Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain R residue 28 GLU Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 54 ARG Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 62 ILE Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 8 ARG Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 14 LYS Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 22 ARG Chi-restraints excluded: chain T residue 23 ARG Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain W residue 19 ASN Chi-restraints excluded: chain W residue 23 ARG Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 69 GLN Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain X residue 121 MET Chi-restraints excluded: chain X residue 123 ARG Chi-restraints excluded: chain X residue 156 MET Chi-restraints excluded: chain X residue 162 ASN Chi-restraints excluded: chain X residue 164 LEU Chi-restraints excluded: chain X residue 168 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 341 optimal weight: 20.0000 chunk 306 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 chunk 367 optimal weight: 2.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN B 110 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN D 119 GLN D 125 HIS D 160 GLN E 56 GLN E 141 GLN F 7 ASN F 11 ASN F 32 ASN F 57 GLN F 64 GLN F 100 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN I 58 HIS I 89 ASN I 124 GLN J 62 HIS K 116 HIS ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 ASN O 62 GLN ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 53 ASN X 69 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.095244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.075909 restraints weight = 149528.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.078811 restraints weight = 70491.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078439 restraints weight = 34149.468| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 58285 Z= 0.308 Angle : 0.810 15.576 86271 Z= 0.413 Chirality : 0.043 0.410 10808 Planarity : 0.006 0.064 5246 Dihedral : 25.513 179.159 27871 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.21 % Favored : 92.25 % Rotamer: Outliers : 11.25 % Allowed : 26.74 % Favored : 62.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % 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: -1.14 (0.16), residues: 2579 helix: 1.55 (0.16), residues: 1007 sheet: -1.83 (0.23), residues: 439 loop : -2.54 (0.16), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 167 HIS 0.008 0.001 HIS I 58 PHE 0.025 0.002 PHE B 28 TYR 0.022 0.002 TYR C 29 ARG 0.007 0.001 ARG M 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 880 time to evaluate : 2.628 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: B 48 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.5654 (tmt) REVERT: B 75 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7686 (ttmt) REVERT: B 106 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7377 (tptt) REVERT: B 110 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8462 (mm-40) REVERT: B 130 ARG cc_start: 0.5720 (OUTLIER) cc_final: 0.5257 (mtm180) REVERT: B 157 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6168 (ppt-90) REVERT: B 178 ARG cc_start: 0.8082 (tpt90) cc_final: 0.7500 (mmt180) REVERT: B 197 VAL cc_start: 0.7350 (t) cc_final: 0.7146 (t) REVERT: B 213 LEU cc_start: 0.8351 (tp) cc_final: 0.7883 (tt) REVERT: B 217 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6990 (mmt90) REVERT: B 222 ILE cc_start: 0.8349 (mt) cc_final: 0.8071 (tp) REVERT: C 94 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8264 (tp) REVERT: C 139 GLN cc_start: 0.9003 (mm110) cc_final: 0.8724 (mm110) REVERT: C 162 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: C 201 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: C 204 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8848 (pp) REVERT: D 10 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8275 (ttm-80) REVERT: D 42 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: D 49 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6992 (mtm180) REVERT: D 60 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7760 (mm-30) REVERT: D 61 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8577 (tttm) REVERT: D 64 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9028 (mt) REVERT: D 65 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8459 (ttp80) REVERT: D 75 PHE cc_start: 0.9333 (t80) cc_final: 0.8741 (t80) REVERT: D 119 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: D 126 ILE cc_start: 0.9342 (mm) cc_final: 0.8867 (mm) REVERT: D 127 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.7774 (p) REVERT: D 187 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7399 (ptt90) REVERT: D 190 ASP cc_start: 0.7871 (t70) cc_final: 0.7644 (m-30) REVERT: D 207 TYR cc_start: 0.8186 (m-10) cc_final: 0.7409 (m-80) REVERT: E 13 ILE cc_start: 0.8890 (pp) cc_final: 0.8501 (pp) REVERT: E 14 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8846 (ptt180) REVERT: E 65 ASN cc_start: 0.8266 (t0) cc_final: 0.8033 (t0) REVERT: E 117 ASP cc_start: 0.6669 (OUTLIER) cc_final: 0.6132 (m-30) REVERT: F 5 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7961 (mt-10) REVERT: F 7 ASN cc_start: 0.8236 (m110) cc_final: 0.7593 (m-40) REVERT: F 11 ASN cc_start: 0.8352 (t0) cc_final: 0.8024 (t0) REVERT: F 36 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7652 (ttp80) REVERT: F 57 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: F 61 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8585 (mt) REVERT: F 69 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: F 74 ASP cc_start: 0.8111 (t0) cc_final: 0.7224 (t0) REVERT: F 78 GLU cc_start: 0.8302 (tp30) cc_final: 0.8068 (mm-30) REVERT: F 92 LYS cc_start: 0.9272 (ttmt) cc_final: 0.8982 (ttmt) REVERT: G 87 VAL cc_start: 0.9426 (t) cc_final: 0.9199 (m) REVERT: G 104 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8732 (mt) REVERT: G 106 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7809 (mm-40) REVERT: G 124 LEU cc_start: 0.8554 (mm) cc_final: 0.8264 (tt) REVERT: H 9 MET cc_start: 0.8783 (ttp) cc_final: 0.8166 (ttp) REVERT: H 33 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7759 (pp20) REVERT: H 41 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8040 (mtm110) REVERT: H 68 ARG cc_start: 0.7441 (tpt-90) cc_final: 0.7058 (tpt-90) REVERT: H 86 ILE cc_start: 0.9044 (mt) cc_final: 0.8758 (mt) REVERT: H 91 ARG cc_start: 0.8431 (ttp80) cc_final: 0.8043 (ttt-90) REVERT: H 132 GLU cc_start: 0.8768 (tt0) cc_final: 0.8559 (tt0) REVERT: I 34 ASN cc_start: 0.8760 (m-40) cc_final: 0.8539 (t0) REVERT: I 38 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6743 (tt0) REVERT: I 62 TYR cc_start: 0.7999 (t80) cc_final: 0.7623 (t80) REVERT: I 70 LYS cc_start: 0.8454 (mmtt) cc_final: 0.7987 (mmtm) REVERT: I 95 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8266 (mtpt) REVERT: I 113 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8494 (mttm) REVERT: I 125 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7016 (p90) REVERT: J 35 SER cc_start: 0.8661 (m) cc_final: 0.8273 (p) REVERT: K 24 SER cc_start: 0.9254 (t) cc_final: 0.8681 (p) REVERT: K 30 VAL cc_start: 0.9531 (t) cc_final: 0.9197 (p) REVERT: K 54 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8539 (mtt90) REVERT: K 55 LYS cc_start: 0.9324 (ttmt) cc_final: 0.8965 (ttpt) REVERT: K 84 VAL cc_start: 0.9277 (OUTLIER) cc_final: 0.8835 (p) REVERT: K 91 ARG cc_start: 0.8745 (ptm-80) cc_final: 0.8254 (ptm-80) REVERT: K 93 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8531 (mm-40) REVERT: K 117 ASN cc_start: 0.8002 (t160) cc_final: 0.7734 (t0) REVERT: L 7 ILE cc_start: 0.9125 (mm) cc_final: 0.8842 (mm) REVERT: M 49 THR cc_start: 0.7799 (m) cc_final: 0.7549 (p) REVERT: M 71 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7463 (mtp-110) REVERT: N 32 SER cc_start: 0.8513 (t) cc_final: 0.7817 (t) REVERT: O 8 LYS cc_start: 0.8805 (tttt) cc_final: 0.8479 (mtpt) REVERT: O 9 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8184 (mm110) REVERT: O 13 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8255 (mp10) REVERT: O 22 THR cc_start: 0.9154 (p) cc_final: 0.8573 (t) REVERT: O 26 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7879 (mp0) REVERT: O 65 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8141 (mtp180) REVERT: P 1 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.7256 (ptt) REVERT: P 8 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8167 (ttt-90) REVERT: P 38 TYR cc_start: 0.8012 (p90) cc_final: 0.7419 (p90) REVERT: P 49 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8684 (tp) REVERT: P 50 LYS cc_start: 0.8630 (tttm) cc_final: 0.8260 (tmtt) REVERT: Q 31 LEU cc_start: 0.9326 (tp) cc_final: 0.9032 (tp) REVERT: Q 46 ASP cc_start: 0.9094 (t0) cc_final: 0.8725 (t0) REVERT: Q 49 GLU cc_start: 0.7571 (tt0) cc_final: 0.7069 (mm-30) REVERT: Q 50 LYS cc_start: 0.7485 (tttt) cc_final: 0.6772 (tptp) REVERT: Q 68 ARG cc_start: 0.8552 (ptm-80) cc_final: 0.8261 (ptm-80) REVERT: Q 86 GLU cc_start: 0.7956 (tp30) cc_final: 0.7664 (mm-30) REVERT: Q 87 LYS cc_start: 0.8763 (mttt) cc_final: 0.8522 (mtmm) REVERT: Q 89 LEU cc_start: 0.8962 (mt) cc_final: 0.8638 (mt) REVERT: R 42 ARG cc_start: 0.8517 (mmm160) cc_final: 0.8157 (mmm160) REVERT: R 69 THR cc_start: 0.9091 (m) cc_final: 0.8866 (p) REVERT: R 72 ARG cc_start: 0.8907 (mtt-85) cc_final: 0.8641 (ttm110) REVERT: S 7 LYS cc_start: 0.5775 (OUTLIER) cc_final: 0.5515 (mttp) REVERT: S 15 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8493 (pp) REVERT: S 17 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8130 (tm-30) REVERT: S 25 LYS cc_start: 0.7364 (mtpp) cc_final: 0.6909 (ttpt) REVERT: S 31 ILE cc_start: 0.7908 (mm) cc_final: 0.7524 (mm) REVERT: S 32 LYS cc_start: 0.8184 (mtpm) cc_final: 0.7952 (mmmm) REVERT: S 38 SER cc_start: 0.8164 (t) cc_final: 0.7483 (p) REVERT: S 52 TYR cc_start: 0.8351 (t80) cc_final: 0.7739 (t80) REVERT: S 78 ARG cc_start: 0.8018 (ptp-110) cc_final: 0.7779 (mtm-85) REVERT: T 23 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8538 (ttp80) REVERT: T 31 SER cc_start: 0.9131 (t) cc_final: 0.8821 (p) REVERT: T 42 GLN cc_start: 0.8923 (mm110) cc_final: 0.8388 (tp40) REVERT: T 64 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: T 83 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8716 (mmm-85) REVERT: V 10 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8139 (tpp-160) REVERT: W 25 LYS cc_start: 0.7583 (tptm) cc_final: 0.7116 (ptpt) REVERT: X 41 MET cc_start: 0.3823 (mmm) cc_final: 0.3407 (ttt) REVERT: X 109 PHE cc_start: 0.7383 (m-80) cc_final: 0.7109 (m-80) REVERT: X 153 LYS cc_start: 0.8259 (mttm) cc_final: 0.7979 (mmtm) REVERT: X 168 VAL cc_start: 0.4503 (OUTLIER) cc_final: 0.4234 (p) outliers start: 247 outliers final: 100 residues processed: 1021 average time/residue: 0.5989 time to fit residues: 974.5508 Evaluate side-chains 876 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 728 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain E residue 14 ARG Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 57 GLN Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 GLN Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 125 TYR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 21 TYR Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 65 ARG Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 75 ARG Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 19 SER Chi-restraints excluded: chain T residue 23 ARG Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 83 ARG Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 121 MET Chi-restraints excluded: chain X residue 156 MET Chi-restraints excluded: chain X residue 162 ASN Chi-restraints excluded: chain X residue 164 LEU Chi-restraints excluded: chain X residue 168 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 137 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 346 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 372 optimal weight: 9.9990 chunk 401 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS C 31 HIS ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 HIS ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN E 73 ASN E 141 GLN F 57 GLN F 64 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN I 58 HIS K 13 GLN K 78 GLN L 8 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 71 GLN T 42 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.093944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.074798 restraints weight = 151108.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.077223 restraints weight = 71641.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.077331 restraints weight = 35953.498| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 58285 Z= 0.429 Angle : 0.814 15.495 86271 Z= 0.411 Chirality : 0.043 0.344 10808 Planarity : 0.006 0.066 5246 Dihedral : 25.132 178.354 27586 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.57 % Favored : 90.97 % Rotamer: Outliers : 11.21 % Allowed : 29.38 % Favored : 59.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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 (0.16), residues: 2579 helix: 1.14 (0.16), residues: 1003 sheet: -1.95 (0.22), residues: 464 loop : -2.24 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP X 65 HIS 0.008 0.001 HIS I 58 PHE 0.020 0.002 PHE O 15 TYR 0.029 0.002 TYR D 4 ARG 0.007 0.001 ARG O 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 787 time to evaluate : 2.612 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: B 48 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.4852 (tpt) REVERT: B 75 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7762 (ttmt) REVERT: B 130 ARG cc_start: 0.5721 (OUTLIER) cc_final: 0.5355 (mtm180) REVERT: B 133 LYS cc_start: 0.7731 (mtmt) cc_final: 0.7461 (tppt) REVERT: B 157 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6327 (ppt-90) REVERT: B 178 ARG cc_start: 0.7833 (tpt90) cc_final: 0.7102 (mmt180) REVERT: B 213 LEU cc_start: 0.8175 (tp) cc_final: 0.7859 (tt) REVERT: C 36 ASP cc_start: 0.8323 (m-30) cc_final: 0.8102 (m-30) REVERT: C 82 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.6332 (pp20) REVERT: C 162 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: C 201 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8450 (m-80) REVERT: C 204 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8865 (pp) REVERT: D 42 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: D 49 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7214 (mtm180) REVERT: D 60 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7977 (mm-30) REVERT: D 64 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9070 (mt) REVERT: D 65 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8638 (ttp80) REVERT: D 75 PHE cc_start: 0.9362 (t80) cc_final: 0.8974 (t80) REVERT: D 127 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7776 (p) REVERT: D 187 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7560 (ptt90) REVERT: D 190 ASP cc_start: 0.8074 (t70) cc_final: 0.7723 (m-30) REVERT: D 207 TYR cc_start: 0.8239 (m-10) cc_final: 0.7689 (m-80) REVERT: E 13 ILE cc_start: 0.8916 (pp) cc_final: 0.8656 (pp) REVERT: E 14 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8789 (ptt-90) REVERT: E 65 ASN cc_start: 0.8422 (t0) cc_final: 0.8182 (t0) REVERT: E 117 ASP cc_start: 0.6364 (OUTLIER) cc_final: 0.6131 (m-30) REVERT: F 5 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7909 (mt-10) REVERT: F 7 ASN cc_start: 0.8194 (m110) cc_final: 0.7677 (m-40) REVERT: F 36 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7898 (ttp80) REVERT: F 69 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: F 74 ASP cc_start: 0.8151 (t0) cc_final: 0.7335 (t0) REVERT: F 86 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7896 (mtt90) REVERT: G 13 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8783 (tm-30) REVERT: G 27 ILE cc_start: 0.9423 (mt) cc_final: 0.9210 (mp) REVERT: G 31 MET cc_start: 0.8246 (ttp) cc_final: 0.7872 (ttm) REVERT: G 151 TYR cc_start: 0.8673 (m-80) cc_final: 0.7855 (m-80) REVERT: H 4 ASP cc_start: 0.7988 (t0) cc_final: 0.7787 (t70) REVERT: H 41 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7927 (mtm110) REVERT: H 68 ARG cc_start: 0.7425 (tpt-90) cc_final: 0.7011 (tpt-90) REVERT: H 91 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8144 (ttt-90) REVERT: H 132 GLU cc_start: 0.8577 (tt0) cc_final: 0.8367 (tt0) REVERT: I 38 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7109 (tt0) REVERT: I 47 LEU cc_start: 0.9108 (mp) cc_final: 0.8669 (pp) REVERT: I 70 LYS cc_start: 0.8336 (mmtt) cc_final: 0.8081 (mmtm) REVERT: I 124 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8079 (tm-30) REVERT: I 125 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7151 (p90) REVERT: J 3 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7655 (tttt) REVERT: J 7 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8209 (ttmm) REVERT: K 12 ARG cc_start: 0.7620 (mmm-85) cc_final: 0.7353 (mtm180) REVERT: K 18 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7621 (mmt90) REVERT: K 24 SER cc_start: 0.9232 (t) cc_final: 0.8677 (p) REVERT: K 30 VAL cc_start: 0.9474 (t) cc_final: 0.9240 (p) REVERT: K 54 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8371 (mtt90) REVERT: K 55 LYS cc_start: 0.9469 (ttmt) cc_final: 0.9184 (ttpt) REVERT: K 84 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.8738 (p) REVERT: K 91 ARG cc_start: 0.8897 (ptm-80) cc_final: 0.8431 (ptm-80) REVERT: L 42 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8386 (p) REVERT: L 78 GLN cc_start: 0.7365 (pp30) cc_final: 0.6848 (pp30) REVERT: M 23 TYR cc_start: 0.8110 (t80) cc_final: 0.7832 (t80) REVERT: M 49 THR cc_start: 0.8048 (m) cc_final: 0.7733 (p) REVERT: M 71 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7419 (mtp-110) REVERT: N 32 SER cc_start: 0.8738 (t) cc_final: 0.8212 (t) REVERT: O 8 LYS cc_start: 0.8866 (tttt) cc_final: 0.8561 (mtpt) REVERT: O 13 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8396 (mp10) REVERT: O 22 THR cc_start: 0.9118 (p) cc_final: 0.8427 (t) REVERT: O 26 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7732 (mp0) REVERT: O 65 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8315 (mtp180) REVERT: P 8 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8293 (ttt-90) REVERT: P 49 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8618 (tp) REVERT: P 50 LYS cc_start: 0.8558 (tttm) cc_final: 0.8256 (tmtt) REVERT: Q 46 ASP cc_start: 0.9101 (t0) cc_final: 0.8862 (t0) REVERT: Q 49 GLU cc_start: 0.7739 (tt0) cc_final: 0.6880 (mm-30) REVERT: Q 50 LYS cc_start: 0.7528 (tttt) cc_final: 0.7096 (tptm) REVERT: Q 86 GLU cc_start: 0.7953 (tp30) cc_final: 0.7689 (mm-30) REVERT: Q 89 LEU cc_start: 0.8918 (mt) cc_final: 0.8353 (mt) REVERT: Q 93 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: R 26 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7962 (pp) REVERT: R 28 GLU cc_start: 0.6837 (tp30) cc_final: 0.6391 (tp30) REVERT: R 72 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8705 (ttm110) REVERT: S 15 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8253 (tt) REVERT: S 17 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7907 (tm-30) REVERT: S 25 LYS cc_start: 0.6876 (mtpp) cc_final: 0.6532 (ttpt) REVERT: S 31 ILE cc_start: 0.7614 (mm) cc_final: 0.7294 (mm) REVERT: S 37 ARG cc_start: 0.8678 (mtm-85) cc_final: 0.8470 (mtm-85) REVERT: S 51 VAL cc_start: 0.8669 (OUTLIER) cc_final: 0.8378 (m) REVERT: S 52 TYR cc_start: 0.8303 (t80) cc_final: 0.7476 (t80) REVERT: S 61 TYR cc_start: 0.5844 (t80) cc_final: 0.5571 (t80) REVERT: S 79 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8581 (p) REVERT: T 31 SER cc_start: 0.9124 (t) cc_final: 0.8762 (p) REVERT: T 42 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8513 (tp40) REVERT: T 64 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: T 68 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8041 (ttmm) REVERT: T 83 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8821 (mmm-85) REVERT: W 25 LYS cc_start: 0.7956 (tptm) cc_final: 0.7433 (ptpt) REVERT: X 60 MET cc_start: 0.5026 (ptp) cc_final: 0.4764 (tpt) REVERT: X 61 ASP cc_start: 0.5634 (OUTLIER) cc_final: 0.5230 (m-30) REVERT: X 65 TRP cc_start: 0.8054 (t60) cc_final: 0.7837 (t60) outliers start: 246 outliers final: 134 residues processed: 914 average time/residue: 0.5712 time to fit residues: 847.6862 Evaluate side-chains 895 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 720 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain E residue 14 ARG Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 86 ARG Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 125 TYR Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 13 GLN Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 21 TYR Chi-restraints excluded: chain O residue 5 LYS Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 65 ARG Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 75 ARG Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 97 SER Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 19 SER Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 83 ARG Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 61 ASP Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 93 LYS Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 121 MET Chi-restraints excluded: chain X residue 156 MET Chi-restraints excluded: chain X residue 162 ASN Chi-restraints excluded: chain X residue 164 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 75 optimal weight: 10.0000 chunk 387 optimal weight: 8.9990 chunk 255 optimal weight: 0.9990 chunk 348 optimal weight: 2.9990 chunk 373 optimal weight: 10.0000 chunk 300 optimal weight: 1.9990 chunk 379 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 403 optimal weight: 40.0000 chunk 18 optimal weight: 10.0000 chunk 370 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN D 123 HIS D 154 ASN E 130 ASN E 141 GLN F 13 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN K 13 GLN K 78 GLN L 8 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.097640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078836 restraints weight = 149166.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.081749 restraints weight = 69049.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.081473 restraints weight = 32201.734| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 58285 Z= 0.232 Angle : 0.684 14.388 86271 Z= 0.346 Chirality : 0.038 0.287 10808 Planarity : 0.005 0.070 5246 Dihedral : 24.883 178.830 27549 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.28 % Favored : 93.33 % Rotamer: Outliers : 8.79 % Allowed : 32.26 % Favored : 58.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.96 (0.16), residues: 2579 helix: 1.27 (0.16), residues: 1001 sheet: -1.68 (0.23), residues: 446 loop : -1.97 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 65 HIS 0.006 0.001 HIS O 42 PHE 0.019 0.002 PHE R 29 TYR 0.023 0.002 TYR D 4 ARG 0.012 0.001 ARG J 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 789 time to evaluate : 2.634 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: B 25 ASN cc_start: 0.8744 (t0) cc_final: 0.8388 (t0) REVERT: B 74 LYS cc_start: 0.8227 (tppt) cc_final: 0.8004 (tptp) REVERT: B 75 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.7694 (ttmt) REVERT: B 90 MET cc_start: 0.8614 (mmp) cc_final: 0.8231 (mmp) REVERT: B 130 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.5739 (mtm180) REVERT: B 133 LYS cc_start: 0.7749 (mtmt) cc_final: 0.7509 (tppt) REVERT: B 157 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6289 (ppt-90) REVERT: B 213 LEU cc_start: 0.8027 (tp) cc_final: 0.7798 (tt) REVERT: C 10 PHE cc_start: 0.9108 (t80) cc_final: 0.8872 (t80) REVERT: C 67 THR cc_start: 0.8712 (m) cc_final: 0.8344 (p) REVERT: C 82 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7921 (pm20) REVERT: C 94 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8460 (tp) REVERT: C 157 ILE cc_start: 0.8452 (mt) cc_final: 0.7375 (mp) REVERT: C 162 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8288 (tp40) REVERT: D 26 CYS cc_start: 0.8671 (OUTLIER) cc_final: 0.7423 (t) REVERT: D 42 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8107 (tm-30) REVERT: D 49 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7126 (mtm180) REVERT: D 60 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7774 (mm-30) REVERT: D 61 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8385 (tttm) REVERT: D 64 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8984 (mt) REVERT: D 68 TYR cc_start: 0.8538 (m-80) cc_final: 0.8195 (m-80) REVERT: D 72 GLU cc_start: 0.8326 (tp30) cc_final: 0.7472 (tp30) REVERT: D 75 PHE cc_start: 0.9308 (t80) cc_final: 0.8971 (t80) REVERT: D 116 GLN cc_start: 0.8922 (tt0) cc_final: 0.8687 (tt0) REVERT: D 127 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8002 (p) REVERT: D 207 TYR cc_start: 0.8060 (m-10) cc_final: 0.7317 (m-80) REVERT: E 13 ILE cc_start: 0.8890 (pp) cc_final: 0.8534 (pp) REVERT: E 14 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8778 (ptt180) REVERT: E 111 GLU cc_start: 0.8335 (tp30) cc_final: 0.8002 (tp30) REVERT: E 117 ASP cc_start: 0.6782 (OUTLIER) cc_final: 0.6545 (m-30) REVERT: F 7 ASN cc_start: 0.8060 (m110) cc_final: 0.7493 (m-40) REVERT: F 64 GLN cc_start: 0.8158 (tt0) cc_final: 0.7846 (tt0) REVERT: F 74 ASP cc_start: 0.8076 (t0) cc_final: 0.7454 (t0) REVERT: F 86 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7737 (mtt90) REVERT: G 18 TYR cc_start: 0.8001 (m-80) cc_final: 0.7742 (m-80) REVERT: G 27 ILE cc_start: 0.9404 (mt) cc_final: 0.9114 (mp) REVERT: G 31 MET cc_start: 0.8073 (ttp) cc_final: 0.7739 (ttm) REVERT: G 96 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8202 (pt0) REVERT: G 144 MET cc_start: 0.7266 (tpp) cc_final: 0.6864 (mmp) REVERT: H 17 THR cc_start: 0.8846 (p) cc_final: 0.8589 (p) REVERT: H 75 ARG cc_start: 0.8317 (mtp85) cc_final: 0.8010 (mtp85) REVERT: H 91 ARG cc_start: 0.8334 (ttp80) cc_final: 0.8054 (ttt-90) REVERT: H 127 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9034 (mp) REVERT: I 10 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7430 (tpt-90) REVERT: I 17 VAL cc_start: 0.8677 (m) cc_final: 0.8465 (m) REVERT: I 47 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8328 (pp) REVERT: I 88 TYR cc_start: 0.7833 (t80) cc_final: 0.7615 (t80) REVERT: I 124 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7876 (tm-30) REVERT: I 125 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7495 (p90) REVERT: J 3 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7692 (tmtt) REVERT: J 7 LYS cc_start: 0.8347 (ttmm) cc_final: 0.8128 (ttmm) REVERT: J 54 PHE cc_start: 0.8132 (t80) cc_final: 0.7890 (t80) REVERT: K 24 SER cc_start: 0.9151 (t) cc_final: 0.8616 (p) REVERT: K 27 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8662 (t0) REVERT: K 30 VAL cc_start: 0.9549 (t) cc_final: 0.9271 (m) REVERT: K 54 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8498 (mtt-85) REVERT: K 55 LYS cc_start: 0.9384 (ttmt) cc_final: 0.9086 (ttpt) REVERT: K 84 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8744 (p) REVERT: K 91 ARG cc_start: 0.8813 (ptm-80) cc_final: 0.8343 (ptm-80) REVERT: K 117 ASN cc_start: 0.7900 (t0) cc_final: 0.7553 (t0) REVERT: L 42 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8398 (p) REVERT: L 59 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7423 (ttm-80) REVERT: L 65 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7148 (tp30) REVERT: L 69 TYR cc_start: 0.8858 (t80) cc_final: 0.8643 (t80) REVERT: L 78 GLN cc_start: 0.7224 (pp30) cc_final: 0.6624 (pp30) REVERT: L 89 ARG cc_start: 0.8529 (ttp-110) cc_final: 0.8204 (ttp80) REVERT: M 23 TYR cc_start: 0.8127 (t80) cc_final: 0.7813 (t80) REVERT: M 71 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7119 (mtp-110) REVERT: N 32 SER cc_start: 0.8383 (t) cc_final: 0.7738 (t) REVERT: N 35 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7532 (mtm-85) REVERT: N 46 GLU cc_start: 0.7706 (tt0) cc_final: 0.7459 (tt0) REVERT: N 50 LYS cc_start: 0.9150 (mmtp) cc_final: 0.8932 (mmtp) REVERT: O 9 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8072 (mm110) REVERT: O 13 GLN cc_start: 0.8606 (mp10) cc_final: 0.8253 (mp10) REVERT: O 22 THR cc_start: 0.9102 (p) cc_final: 0.8344 (t) REVERT: P 8 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8292 (ttt-90) REVERT: P 38 TYR cc_start: 0.7830 (p90) cc_final: 0.7133 (p90) REVERT: P 50 LYS cc_start: 0.8507 (tttm) cc_final: 0.7956 (tttp) REVERT: P 53 VAL cc_start: 0.8255 (p) cc_final: 0.7921 (m) REVERT: Q 13 ASP cc_start: 0.7450 (t70) cc_final: 0.6726 (t0) REVERT: Q 50 LYS cc_start: 0.7587 (tttt) cc_final: 0.7274 (tptm) REVERT: Q 68 ARG cc_start: 0.8034 (ptm-80) cc_final: 0.7625 (ptm-80) REVERT: Q 74 LEU cc_start: 0.9040 (tp) cc_final: 0.8834 (tp) REVERT: Q 87 LYS cc_start: 0.8845 (mttt) cc_final: 0.8335 (mtpp) REVERT: Q 89 LEU cc_start: 0.8916 (mt) cc_final: 0.8343 (mt) REVERT: Q 93 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7820 (mp10) REVERT: R 72 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8624 (ttm110) REVERT: S 12 ASP cc_start: 0.6171 (m-30) cc_final: 0.5294 (m-30) REVERT: S 15 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8118 (tt) REVERT: S 17 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7916 (tm-30) REVERT: S 37 ARG cc_start: 0.8623 (mtm-85) cc_final: 0.8352 (mtm-85) REVERT: S 38 SER cc_start: 0.8211 (t) cc_final: 0.7737 (p) REVERT: S 40 ILE cc_start: 0.9100 (mt) cc_final: 0.8657 (tt) REVERT: S 52 TYR cc_start: 0.8046 (t80) cc_final: 0.7352 (t80) REVERT: S 61 TYR cc_start: 0.6117 (t80) cc_final: 0.5786 (t80) REVERT: T 31 SER cc_start: 0.9049 (t) cc_final: 0.8691 (p) REVERT: T 42 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8374 (tp40) REVERT: T 83 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8807 (mmm-85) REVERT: V 10 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8086 (tpp-160) REVERT: W 25 LYS cc_start: 0.7956 (tptm) cc_final: 0.7482 (ptpt) REVERT: W 56 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7284 (tt0) outliers start: 193 outliers final: 109 residues processed: 889 average time/residue: 0.5716 time to fit residues: 823.9668 Evaluate side-chains 871 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 729 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 14 ARG Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 86 ARG Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain I residue 10 ARG Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 125 TYR Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 64 TRP Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 21 TYR Chi-restraints excluded: chain O residue 5 LYS Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 75 ARG Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 97 SER Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 19 SER Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain T residue 83 ARG Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 56 GLU Chi-restraints excluded: chain X residue 5 TYR Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 48 VAL Chi-restraints excluded: chain X residue 93 LYS Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 121 MET Chi-restraints excluded: chain X residue 156 MET Chi-restraints excluded: chain X residue 162 ASN Chi-restraints excluded: chain X residue 164 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 225 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 193 optimal weight: 0.0040 chunk 104 optimal weight: 10.0000 chunk 222 optimal weight: 0.9980 chunk 312 optimal weight: 0.4980 chunk 274 optimal weight: 0.8980 chunk 360 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN E 130 ASN E 141 GLN F 18 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS J 56 HIS K 13 GLN L 8 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 ASN T 9 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.101896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083753 restraints weight = 148344.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.086227 restraints weight = 69457.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.086301 restraints weight = 35904.412| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 58285 Z= 0.161 Angle : 0.633 13.695 86271 Z= 0.319 Chirality : 0.035 0.305 10808 Planarity : 0.005 0.053 5246 Dihedral : 24.616 179.908 27510 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.24 % Favored : 93.33 % Rotamer: Outliers : 7.47 % Allowed : 32.98 % Favored : 59.54 % 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: -0.79 (0.16), residues: 2579 helix: 1.30 (0.16), residues: 991 sheet: -1.40 (0.24), residues: 431 loop : -1.83 (0.18), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP X 65 HIS 0.007 0.001 HIS I 58 PHE 0.022 0.002 PHE G 62 TYR 0.021 0.002 TYR P 38 ARG 0.009 0.001 ARG J 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 802 time to evaluate : 2.607 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: B 25 ASN cc_start: 0.8654 (t0) cc_final: 0.8383 (t0) REVERT: B 75 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7951 (ttmt) REVERT: B 90 MET cc_start: 0.8627 (mmp) cc_final: 0.8286 (mmp) REVERT: B 130 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.5545 (mtm180) REVERT: B 133 LYS cc_start: 0.7802 (mtmt) cc_final: 0.7552 (tppt) REVERT: B 157 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6017 (ppt-90) REVERT: B 169 LYS cc_start: 0.8205 (tmtt) cc_final: 0.7976 (tptp) REVERT: B 213 LEU cc_start: 0.8088 (tp) cc_final: 0.7863 (tt) REVERT: C 67 THR cc_start: 0.8586 (m) cc_final: 0.8306 (p) REVERT: C 94 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8223 (tp) REVERT: C 162 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8352 (tp40) REVERT: D 15 GLU cc_start: 0.7573 (mp0) cc_final: 0.7331 (mp0) REVERT: D 42 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: D 47 ARG cc_start: 0.8079 (ttt90) cc_final: 0.7860 (ttt180) REVERT: D 49 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7146 (mtm180) REVERT: D 60 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7715 (mm-30) REVERT: D 61 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8791 (tttm) REVERT: D 64 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9012 (mt) REVERT: D 75 PHE cc_start: 0.9309 (t80) cc_final: 0.9038 (t80) REVERT: D 96 LEU cc_start: 0.9355 (tp) cc_final: 0.9053 (mm) REVERT: D 126 ILE cc_start: 0.9115 (mm) cc_final: 0.8721 (mm) REVERT: D 127 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.7972 (p) REVERT: D 187 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7548 (ptt90) REVERT: D 190 ASP cc_start: 0.7968 (t0) cc_final: 0.7729 (t0) REVERT: D 207 TYR cc_start: 0.8103 (m-10) cc_final: 0.7331 (m-80) REVERT: E 13 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8398 (pp) REVERT: E 14 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8645 (ptt180) REVERT: E 71 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7656 (mp) REVERT: E 98 THR cc_start: 0.8332 (m) cc_final: 0.8012 (p) REVERT: E 111 GLU cc_start: 0.8299 (tp30) cc_final: 0.7961 (tp30) REVERT: F 7 ASN cc_start: 0.8000 (m110) cc_final: 0.7565 (m-40) REVERT: F 64 GLN cc_start: 0.7904 (tt0) cc_final: 0.7696 (tt0) REVERT: F 69 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: F 74 ASP cc_start: 0.7917 (t0) cc_final: 0.7166 (t0) REVERT: F 86 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7519 (mtt90) REVERT: F 96 PRO cc_start: 0.8100 (Cg_endo) cc_final: 0.7897 (Cg_exo) REVERT: G 13 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8597 (tm-30) REVERT: G 18 TYR cc_start: 0.7958 (m-80) cc_final: 0.7715 (m-80) REVERT: G 27 ILE cc_start: 0.9441 (mt) cc_final: 0.9143 (mp) REVERT: G 31 MET cc_start: 0.7907 (ttp) cc_final: 0.7538 (ttm) REVERT: G 73 MET cc_start: 0.7936 (mmm) cc_final: 0.7511 (mmm) REVERT: G 74 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7658 (tm-30) REVERT: G 144 MET cc_start: 0.7176 (tpp) cc_final: 0.6652 (mmp) REVERT: H 49 GLU cc_start: 0.7099 (pt0) cc_final: 0.6601 (pt0) REVERT: H 52 ASP cc_start: 0.7425 (t0) cc_final: 0.7179 (t0) REVERT: H 103 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8376 (p) REVERT: H 126 LYS cc_start: 0.8123 (mmpt) cc_final: 0.7640 (mmmt) REVERT: H 127 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9036 (mp) REVERT: I 3 GLN cc_start: 0.6424 (tt0) cc_final: 0.6164 (tt0) REVERT: I 12 GLU cc_start: 0.7482 (tp30) cc_final: 0.7241 (tp30) REVERT: I 47 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8450 (pp) REVERT: I 99 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7313 (mm) REVERT: I 124 GLN cc_start: 0.8457 (tt0) cc_final: 0.7933 (tm-30) REVERT: J 3 LYS cc_start: 0.8230 (pttm) cc_final: 0.7796 (tmtt) REVERT: J 65 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8448 (tm) REVERT: J 76 ASN cc_start: 0.6023 (p0) cc_final: 0.5356 (p0) REVERT: K 24 SER cc_start: 0.8998 (t) cc_final: 0.8476 (p) REVERT: K 30 VAL cc_start: 0.9410 (t) cc_final: 0.9194 (m) REVERT: K 54 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8373 (mtt-85) REVERT: K 55 LYS cc_start: 0.9321 (ttmt) cc_final: 0.9022 (ttpt) REVERT: K 84 VAL cc_start: 0.9041 (t) cc_final: 0.8600 (p) REVERT: K 108 ILE cc_start: 0.8886 (mp) cc_final: 0.8564 (mt) REVERT: K 117 ASN cc_start: 0.7430 (t0) cc_final: 0.7039 (t0) REVERT: L 42 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8300 (p) REVERT: L 86 ARG cc_start: 0.8495 (ttp80) cc_final: 0.8211 (ttp-170) REVERT: L 89 ARG cc_start: 0.8496 (ttp-110) cc_final: 0.8187 (ttp80) REVERT: M 101 GLN cc_start: 0.7460 (mt0) cc_final: 0.7068 (mt0) REVERT: N 8 GLU cc_start: 0.8447 (pp20) cc_final: 0.7916 (pt0) REVERT: N 16 PHE cc_start: 0.8299 (m-80) cc_final: 0.8030 (m-80) REVERT: N 32 SER cc_start: 0.8332 (t) cc_final: 0.7620 (t) REVERT: N 35 ARG cc_start: 0.8031 (mtt90) cc_final: 0.7618 (mtm-85) REVERT: O 9 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7889 (mm110) REVERT: O 13 GLN cc_start: 0.8505 (mp10) cc_final: 0.8236 (mp10) REVERT: O 62 GLN cc_start: 0.8648 (tp-100) cc_final: 0.8093 (tp40) REVERT: P 8 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8119 (ttt-90) REVERT: P 50 LYS cc_start: 0.8510 (tttm) cc_final: 0.8085 (tttp) REVERT: Q 71 PHE cc_start: 0.9165 (m-80) cc_final: 0.8910 (m-10) REVERT: Q 87 LYS cc_start: 0.8841 (mttt) cc_final: 0.8538 (ttmm) REVERT: Q 89 LEU cc_start: 0.8895 (mt) cc_final: 0.8365 (mt) REVERT: Q 93 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: R 28 GLU cc_start: 0.6784 (tp30) cc_final: 0.6546 (tp30) REVERT: S 5 LEU cc_start: 0.6984 (mt) cc_final: 0.6668 (mt) REVERT: S 12 ASP cc_start: 0.6310 (m-30) cc_final: 0.5570 (m-30) REVERT: S 15 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8207 (tt) REVERT: S 38 SER cc_start: 0.7964 (t) cc_final: 0.7549 (p) REVERT: S 40 ILE cc_start: 0.9046 (mt) cc_final: 0.8634 (tt) REVERT: S 52 TYR cc_start: 0.7780 (t80) cc_final: 0.7275 (t80) REVERT: S 61 TYR cc_start: 0.5990 (t80) cc_final: 0.5780 (t80) REVERT: T 31 SER cc_start: 0.9029 (t) cc_final: 0.8636 (p) REVERT: T 42 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8306 (tp40) REVERT: T 46 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: T 50 GLU cc_start: 0.7971 (mp0) cc_final: 0.7760 (mp0) REVERT: T 83 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8714 (mmm-85) REVERT: V 10 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8041 (tpp-160) REVERT: V 20 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7795 (ttmt) REVERT: W 25 LYS cc_start: 0.7903 (tptm) cc_final: 0.7493 (ptpt) REVERT: W 46 ARG cc_start: 0.7404 (mmt180) cc_final: 0.6907 (mmt180) REVERT: W 51 ASP cc_start: 0.5031 (t0) cc_final: 0.4754 (t0) REVERT: X 41 MET cc_start: 0.6639 (mpp) cc_final: 0.3160 (tpp) REVERT: X 60 MET cc_start: 0.5181 (tpt) cc_final: 0.4977 (tpt) REVERT: X 164 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6969 (mt) outliers start: 164 outliers final: 84 residues processed: 885 average time/residue: 0.5709 time to fit residues: 822.1915 Evaluate side-chains 865 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 750 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 14 ARG Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 86 ARG Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 13 GLN Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 64 TRP Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 21 TYR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 75 ARG Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 97 SER Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 19 SER Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain T residue 83 ARG Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 20 LYS Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain X residue 5 TYR Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 48 VAL Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 93 LYS Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 162 ASN Chi-restraints excluded: chain X residue 164 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 295 optimal weight: 8.9990 chunk 208 optimal weight: 10.0000 chunk 350 optimal weight: 0.3980 chunk 225 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 399 optimal weight: 0.0770 chunk 296 optimal weight: 6.9990 chunk 333 optimal weight: 20.0000 chunk 305 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 overall best weight: 3.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN B 204 ASN C 6 HIS D 74 GLN D 103 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN E 130 ASN F 18 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN G 109 ASN I 58 HIS J 68 HIS ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.099124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.080330 restraints weight = 148498.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.082899 restraints weight = 71654.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.082898 restraints weight = 34188.940| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 58285 Z= 0.244 Angle : 0.664 14.699 86271 Z= 0.334 Chirality : 0.036 0.277 10808 Planarity : 0.005 0.068 5246 Dihedral : 24.570 179.982 27465 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.24 % Favored : 93.49 % Rotamer: Outliers : 7.20 % Allowed : 34.03 % Favored : 58.77 % 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: -0.86 (0.16), residues: 2579 helix: 1.18 (0.16), residues: 993 sheet: -1.45 (0.24), residues: 438 loop : -1.80 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 65 HIS 0.008 0.001 HIS I 58 PHE 0.028 0.002 PHE I 37 TYR 0.020 0.002 TYR M 59 ARG 0.009 0.001 ARG K 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 753 time to evaluate : 3.474 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: B 21 ARG cc_start: 0.6567 (mtp180) cc_final: 0.6139 (ttt180) REVERT: B 25 ASN cc_start: 0.8643 (t0) cc_final: 0.8340 (t0) REVERT: B 90 MET cc_start: 0.8521 (mmp) cc_final: 0.8185 (mmp) REVERT: B 130 ARG cc_start: 0.5770 (OUTLIER) cc_final: 0.5344 (mtm180) REVERT: B 133 LYS cc_start: 0.7715 (mtmt) cc_final: 0.7480 (tppt) REVERT: B 213 LEU cc_start: 0.8014 (tp) cc_final: 0.7767 (tt) REVERT: C 67 THR cc_start: 0.8648 (m) cc_final: 0.8291 (p) REVERT: C 94 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8647 (tp) REVERT: C 162 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8347 (tp40) REVERT: D 10 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7556 (ttm-80) REVERT: D 26 CYS cc_start: 0.8968 (OUTLIER) cc_final: 0.7762 (t) REVERT: D 42 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: D 47 ARG cc_start: 0.8082 (ttt90) cc_final: 0.7826 (ttt180) REVERT: D 49 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7147 (mtm180) REVERT: D 60 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7824 (mm-30) REVERT: D 61 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8729 (tttm) REVERT: D 64 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9006 (mt) REVERT: D 75 PHE cc_start: 0.9325 (t80) cc_final: 0.8991 (t80) REVERT: D 96 LEU cc_start: 0.9364 (tp) cc_final: 0.9078 (mm) REVERT: D 126 ILE cc_start: 0.9177 (mm) cc_final: 0.8660 (mm) REVERT: D 127 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8147 (p) REVERT: D 190 ASP cc_start: 0.7946 (t0) cc_final: 0.7595 (t0) REVERT: D 207 TYR cc_start: 0.8165 (m-10) cc_final: 0.7528 (m-10) REVERT: E 13 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8484 (pp) REVERT: E 14 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8673 (ptt180) REVERT: E 71 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7722 (mp) REVERT: E 111 GLU cc_start: 0.8316 (tp30) cc_final: 0.8013 (tp30) REVERT: E 117 ASP cc_start: 0.6918 (m-30) cc_final: 0.6518 (m-30) REVERT: F 5 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7442 (mt-10) REVERT: F 7 ASN cc_start: 0.8024 (m110) cc_final: 0.7563 (m-40) REVERT: F 18 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: F 64 GLN cc_start: 0.8111 (tt0) cc_final: 0.7836 (tt0) REVERT: F 69 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: F 74 ASP cc_start: 0.8075 (t0) cc_final: 0.7256 (t0) REVERT: F 86 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7534 (mtt90) REVERT: F 96 PRO cc_start: 0.8218 (Cg_endo) cc_final: 0.8005 (Cg_exo) REVERT: G 27 ILE cc_start: 0.9434 (mt) cc_final: 0.9154 (mp) REVERT: G 31 MET cc_start: 0.8064 (ttp) cc_final: 0.7542 (ttm) REVERT: G 74 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7729 (tm-30) REVERT: H 49 GLU cc_start: 0.7358 (pt0) cc_final: 0.6983 (pt0) REVERT: H 70 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7669 (pp30) REVERT: H 126 LYS cc_start: 0.8103 (mmpt) cc_final: 0.7636 (mmmt) REVERT: I 10 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8217 (tpt90) REVERT: I 47 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8351 (pp) REVERT: I 124 GLN cc_start: 0.8416 (tt0) cc_final: 0.7880 (tm-30) REVERT: J 3 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7855 (tmtt) REVERT: J 35 SER cc_start: 0.7944 (t) cc_final: 0.7466 (p) REVERT: J 76 ASN cc_start: 0.6375 (p0) cc_final: 0.5841 (p0) REVERT: K 24 SER cc_start: 0.9039 (t) cc_final: 0.8520 (p) REVERT: K 27 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8632 (t0) REVERT: K 30 VAL cc_start: 0.9436 (t) cc_final: 0.9196 (m) REVERT: K 54 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8349 (mtt-85) REVERT: K 55 LYS cc_start: 0.9400 (ttmt) cc_final: 0.9093 (ttpt) REVERT: K 84 VAL cc_start: 0.9092 (t) cc_final: 0.8618 (p) REVERT: K 91 ARG cc_start: 0.8764 (ptm-80) cc_final: 0.8292 (ptm-80) REVERT: K 93 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8558 (mm-40) REVERT: K 117 ASN cc_start: 0.7558 (t0) cc_final: 0.7119 (t0) REVERT: L 42 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8409 (p) REVERT: L 89 ARG cc_start: 0.8481 (ttp-110) cc_final: 0.8188 (ttp80) REVERT: M 101 GLN cc_start: 0.7682 (mt0) cc_final: 0.7261 (mt0) REVERT: N 32 SER cc_start: 0.8589 (t) cc_final: 0.7898 (t) REVERT: N 35 ARG cc_start: 0.8067 (mtt90) cc_final: 0.7488 (mtm-85) REVERT: N 46 GLU cc_start: 0.7843 (tt0) cc_final: 0.7616 (tt0) REVERT: O 9 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8091 (mm110) REVERT: O 13 GLN cc_start: 0.8557 (mp10) cc_final: 0.8201 (mp10) REVERT: O 22 THR cc_start: 0.9014 (p) cc_final: 0.8309 (t) REVERT: P 8 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8181 (ttt-90) REVERT: P 50 LYS cc_start: 0.8518 (tttm) cc_final: 0.8058 (tttp) REVERT: P 53 VAL cc_start: 0.8212 (p) cc_final: 0.7953 (m) REVERT: Q 50 LYS cc_start: 0.8132 (pttt) cc_final: 0.7874 (pttt) REVERT: Q 87 LYS cc_start: 0.8867 (mttt) cc_final: 0.8514 (ttmm) REVERT: Q 89 LEU cc_start: 0.8846 (mt) cc_final: 0.8244 (mt) REVERT: Q 93 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: R 62 GLU cc_start: 0.8609 (pm20) cc_final: 0.8398 (pm20) REVERT: R 82 THR cc_start: 0.8926 (m) cc_final: 0.8666 (p) REVERT: S 5 LEU cc_start: 0.7248 (mt) cc_final: 0.6877 (mt) REVERT: S 37 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.8140 (mtp85) REVERT: S 61 TYR cc_start: 0.6085 (t80) cc_final: 0.5733 (t80) REVERT: T 31 SER cc_start: 0.9040 (t) cc_final: 0.8662 (p) REVERT: T 42 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8332 (tp40) REVERT: T 68 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.8029 (ttmm) REVERT: T 83 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8622 (mmm-85) REVERT: V 10 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8127 (tpp-160) REVERT: W 25 LYS cc_start: 0.7942 (tptm) cc_final: 0.7491 (ptpt) REVERT: W 39 LYS cc_start: 0.7984 (mtpp) cc_final: 0.7572 (mttm) REVERT: W 51 ASP cc_start: 0.5218 (t0) cc_final: 0.4774 (t0) REVERT: X 111 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8433 (mp10) REVERT: X 121 MET cc_start: 0.6701 (tpp) cc_final: 0.6428 (tpp) outliers start: 158 outliers final: 94 residues processed: 834 average time/residue: 0.6040 time to fit residues: 825.9168 Evaluate side-chains 836 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 712 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 14 ARG Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 18 GLN Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 86 ARG Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain I residue 10 ARG Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 GLU Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 64 TRP Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 21 TYR Chi-restraints excluded: chain O residue 5 LYS Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 75 ARG Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain T residue 19 SER Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain T residue 83 ARG Chi-restraints excluded: chain V residue 10 ARG Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain X residue 5 TYR Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 48 VAL Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 93 LYS Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 162 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9284 > 50: distance: 116 - 252: 33.778 distance: 119 - 249: 33.620 distance: 128 - 235: 35.493 distance: 170 - 175: 29.217 distance: 175 - 176: 21.008 distance: 176 - 179: 18.928 distance: 177 - 178: 40.038 distance: 177 - 183: 56.838 distance: 179 - 180: 44.949 distance: 180 - 181: 57.213 distance: 180 - 182: 55.045 distance: 183 - 184: 37.097 distance: 184 - 185: 3.235 distance: 184 - 187: 38.959 distance: 185 - 186: 56.792 distance: 187 - 188: 43.573 distance: 188 - 189: 41.343 distance: 188 - 190: 19.962 distance: 189 - 191: 52.348 distance: 191 - 193: 8.020 distance: 193 - 194: 50.674 distance: 195 - 196: 39.512 distance: 196 - 197: 40.571 distance: 197 - 199: 64.461 distance: 199 - 200: 52.337 distance: 200 - 201: 39.590 distance: 200 - 203: 19.359 distance: 201 - 202: 20.112 distance: 201 - 208: 40.174 distance: 203 - 204: 21.828 distance: 204 - 205: 40.269 distance: 206 - 207: 57.440 distance: 208 - 209: 38.713 distance: 209 - 210: 40.340 distance: 209 - 212: 40.472 distance: 210 - 211: 39.660 distance: 210 - 215: 38.791 distance: 212 - 213: 29.479 distance: 212 - 214: 11.093 distance: 216 - 219: 56.376 distance: 217 - 223: 56.564 distance: 219 - 220: 58.079 distance: 219 - 221: 55.552 distance: 220 - 222: 38.797 distance: 223 - 224: 39.558 distance: 224 - 225: 49.024 distance: 225 - 226: 41.173 distance: 225 - 232: 14.583 distance: 228 - 229: 57.532 distance: 229 - 230: 39.190 distance: 230 - 231: 20.387 distance: 233 - 234: 39.042 distance: 233 - 236: 56.970 distance: 234 - 235: 40.928 distance: 234 - 243: 12.107 distance: 236 - 237: 39.403 distance: 238 - 239: 47.205 distance: 239 - 240: 14.951 distance: 240 - 241: 39.788 distance: 240 - 242: 40.247 distance: 243 - 244: 11.081 distance: 244 - 245: 67.534 distance: 244 - 247: 40.251 distance: 245 - 246: 40.790 distance: 245 - 249: 39.662 distance: 247 - 248: 53.370 distance: 249 - 250: 38.403 distance: 250 - 251: 55.465 distance: 250 - 253: 57.026 distance: 251 - 252: 34.915 distance: 251 - 258: 30.528 distance: 253 - 254: 41.465 distance: 254 - 255: 38.886 distance: 255 - 256: 40.697 distance: 256 - 257: 41.654