Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 19 11:50:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj6_10212/08_2023/6sj6_10212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj6_10212/08_2023/6sj6_10212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj6_10212/08_2023/6sj6_10212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj6_10212/08_2023/6sj6_10212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj6_10212/08_2023/6sj6_10212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj6_10212/08_2023/6sj6_10212.pdb" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 K 3 8.98 5 P 2683 5.49 5 Mg 56 5.21 5 S 46 5.16 5 C 38599 2.51 5 N 14481 2.21 5 O 22428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 176": "NH1" <-> "NH2" Residue "E TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "F ARG 41": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F ARG 107": "NH1" <-> "NH2" Residue "F ARG 168": "NH1" <-> "NH2" Residue "M ARG 28": "NH1" <-> "NH2" Residue "M ARG 95": "NH1" <-> "NH2" Residue "M ARG 144": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 33": "NH1" <-> "NH2" Residue "O ARG 41": "NH1" <-> "NH2" Residue "O ARG 47": "NH1" <-> "NH2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 45": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P ARG 115": "NH1" <-> "NH2" Residue "P ARG 134": "NH1" <-> "NH2" Residue "Q ARG 96": "NH1" <-> "NH2" Residue "S ARG 23": "NH1" <-> "NH2" Residue "S ARG 33": "NH1" <-> "NH2" Residue "T ARG 48": "NH1" <-> "NH2" Residue "U ARG 84": "NH1" <-> "NH2" Residue "V ARG 11": "NH1" <-> "NH2" Residue "W ARG 4": "NH1" <-> "NH2" Residue "W ARG 9": "NH1" <-> "NH2" Residue "W ARG 64": "NH1" <-> "NH2" Residue "Y ARG 15": "NH1" <-> "NH2" Residue "Y ARG 53": "NH1" <-> "NH2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "Z PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 79": "NH1" <-> "NH2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "0 ARG 17": "NH1" <-> "NH2" Residue "0 ARG 18": "NH1" <-> "NH2" Residue "0 ARG 37": "NH1" <-> "NH2" Residue "0 ARG 52": "NH1" <-> "NH2" Residue "1 ARG 7": "NH1" <-> "NH2" Residue "1 ARG 52": "NH1" <-> "NH2" Residue "1 ARG 58": "NH1" <-> "NH2" Residue "1 ARG 60": "NH1" <-> "NH2" Residue "6 ARG 40": "NH1" <-> "NH2" Residue "7 ARG 24": "NH1" <-> "NH2" Residue "7 ARG 48": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 78296 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 55399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2585, 55399 Inner-chain residues flagged as termini: ['pdbres=" U A 233 "', 'pdbres=" U A 690 "', 'pdbres=" C A 764 "', 'pdbres=" G A 937 "', 'pdbres=" G A1156 "', 'pdbres=" C A1595 "', 'pdbres=" A A1923 "', 'pdbres=" A A1954 "', 'pdbres=" C A2210 "', 'pdbres=" C A2241 "', 'pdbres=" U A2825 "'] Classifications: {'RNA': 2585} Modifications used: {'5*END': 12, 'rna2p_pur': 283, 'rna2p_pyr': 137, 'rna3p_pur': 1201, 'rna3p_pyr': 964} Link IDs: {'rna2p': 420, 'rna3p': 2164} Chain: "B" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2380 Inner-chain residues flagged as termini: ['pdbres=" A B 44 "'] Classifications: {'RNA': 112} Modifications used: {'5*END': 2, 'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 53, 'rna3p_pyr': 44} Link IDs: {'rna2p': 15, 'rna3p': 96} Chain: "D" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1863 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 10, 'TRANS': 231} Chain breaks: 1 Chain: "E" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1637 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 8, 'TRANS': 207} Chain: "F" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1540 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 6, 'PTRANS': 9, 'TRANS': 187} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1151 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "N" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "O" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1099 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "P" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1097 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "Q" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain: "R" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 109} Chain: "S" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 837 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "T" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "U" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "V" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "W" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 725 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "X" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 738 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "Y" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 458 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 2 Chain: "Z" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 597 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "0" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 353 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "1" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "2" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 441 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "4" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 285 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain breaks: 1 Chain: "6" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "7" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 500 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "9" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 908 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Unusual residues: {' K': 3, ' MG': 56} Classifications: {'undetermined': 59} Link IDs: {None: 58} Time building chain proxies: 28.11, per 1000 atoms: 0.36 Number of scatterers: 78296 At special positions: 0 Unit cell: (211.068, 229.944, 207.636, 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) K 3 19.00 S 46 16.00 P 2683 15.00 Mg 56 11.99 O 22428 8.00 N 14481 7.00 C 38599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.43 Conformation dependent library (CDL) restraints added in 2.7 seconds 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4768 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 36 sheets defined 20.1% alpha, 13.7% beta 373 base pairs and 1309 stacking pairs defined. Time for finding SS restraints: 25.09 Creating SS restraints... Processing helix chain 'D' and resid 206 through 214 removed outlier: 3.601A pdb=" N SER D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY D 214 " --> pdb=" O SER D 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 removed outlier: 3.676A pdb=" N HIS E 76 " --> pdb=" O PRO E 72 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 81 No H-bonds generated for 'chain 'E' and resid 79 through 81' Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'F' and resid 29 through 34 removed outlier: 3.944A pdb=" N LEU F 33 " --> pdb=" O ASN F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 42 Processing helix chain 'F' and resid 103 through 118 removed outlier: 4.824A pdb=" N ALA F 109 " --> pdb=" O MET F 105 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE F 116 " --> pdb=" O SER F 112 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 140 through 145 removed outlier: 3.958A pdb=" N SER F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 199 Processing helix chain 'M' and resid 25 through 34 removed outlier: 4.236A pdb=" N GLU M 32 " --> pdb=" O ARG M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 95 removed outlier: 3.575A pdb=" N ARG M 94 " --> pdb=" O GLY M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 105 removed outlier: 3.859A pdb=" N LEU M 101 " --> pdb=" O ASN M 97 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE M 102 " --> pdb=" O PRO M 98 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU M 103 " --> pdb=" O GLU M 99 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER M 105 " --> pdb=" O LEU M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 121 Processing helix chain 'N' and resid 103 through 107 Processing helix chain 'N' and resid 111 through 116 removed outlier: 3.568A pdb=" N VAL N 115 " --> pdb=" O PHE N 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 83 removed outlier: 3.797A pdb=" N ASN O 83 " --> pdb=" O ASP O 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 80 through 83' Processing helix chain 'O' and resid 92 through 99 removed outlier: 3.649A pdb=" N SER O 99 " --> pdb=" O LEU O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 137 Processing helix chain 'P' and resid 44 through 56 removed outlier: 3.590A pdb=" N SER P 49 " --> pdb=" O ARG P 45 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA P 53 " --> pdb=" O SER P 49 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET P 54 " --> pdb=" O ALA P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 123 removed outlier: 4.023A pdb=" N ALA P 114 " --> pdb=" O SER P 110 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA P 121 " --> pdb=" O ALA P 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER P 122 " --> pdb=" O LEU P 118 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HIS P 123 " --> pdb=" O ARG P 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 28 removed outlier: 4.375A pdb=" N ALA Q 15 " --> pdb=" O ASP Q 11 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG Q 18 " --> pdb=" O LYS Q 14 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP Q 19 " --> pdb=" O ALA Q 15 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR Q 22 " --> pdb=" O ARG Q 18 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE Q 25 " --> pdb=" O ALA Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 38 Processing helix chain 'Q' and resid 39 through 44 removed outlier: 3.818A pdb=" N VAL Q 44 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 54 removed outlier: 3.532A pdb=" N ILE Q 48 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR Q 49 " --> pdb=" O GLU Q 45 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU Q 50 " --> pdb=" O LYS Q 46 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS Q 53 " --> pdb=" O THR Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 62 Processing helix chain 'Q' and resid 88 through 93 Processing helix chain 'R' and resid 58 through 62 removed outlier: 3.881A pdb=" N ASP R 62 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 74 removed outlier: 3.869A pdb=" N ALA R 73 " --> pdb=" O LYS R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 84 removed outlier: 3.653A pdb=" N LYS R 82 " --> pdb=" O GLU R 78 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS R 83 " --> pdb=" O ALA R 79 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA R 84 " --> pdb=" O ILE R 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 78 through 84' Processing helix chain 'R' and resid 104 through 115 removed outlier: 3.906A pdb=" N ALA R 111 " --> pdb=" O ALA R 107 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA R 112 " --> pdb=" O LEU R 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU R 114 " --> pdb=" O GLU R 110 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 11 removed outlier: 3.825A pdb=" N VAL S 10 " --> pdb=" O LEU S 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 14 Processing helix chain 'T' and resid 14 through 19 removed outlier: 3.973A pdb=" N ILE T 18 " --> pdb=" O ARG T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.506A pdb=" N HIS T 29 " --> pdb=" O GLY T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 50 removed outlier: 4.304A pdb=" N GLN T 37 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET T 40 " --> pdb=" O LYS T 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS T 41 " --> pdb=" O GLN T 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY T 43 " --> pdb=" O VAL T 39 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG T 48 " --> pdb=" O GLN T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 64 removed outlier: 4.311A pdb=" N ARG T 58 " --> pdb=" O LYS T 54 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS T 59 " --> pdb=" O ARG T 55 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU T 60 " --> pdb=" O ASP T 56 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE T 62 " --> pdb=" O ARG T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 72 removed outlier: 3.530A pdb=" N GLN T 71 " --> pdb=" O ALA T 67 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N HIS T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 67 through 72' Processing helix chain 'T' and resid 76 through 87 removed outlier: 3.515A pdb=" N LEU T 83 " --> pdb=" O LEU T 79 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS T 84 " --> pdb=" O MET T 80 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS T 85 " --> pdb=" O ASN T 81 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA T 86 " --> pdb=" O GLY T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 100 Processing helix chain 'T' and resid 103 through 116 removed outlier: 3.735A pdb=" N ALA T 113 " --> pdb=" O LEU T 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 22 removed outlier: 3.525A pdb=" N VAL V 17 " --> pdb=" O ALA V 13 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU V 19 " --> pdb=" O ARG V 15 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL V 20 " --> pdb=" O LYS V 16 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU V 21 " --> pdb=" O VAL V 17 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP V 22 " --> pdb=" O ARG V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 32 through 38 Processing helix chain 'V' and resid 43 through 52 removed outlier: 4.374A pdb=" N LYS V 49 " --> pdb=" O PRO V 45 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL V 50 " --> pdb=" O VAL V 46 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU V 51 " --> pdb=" O ILE V 47 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET V 52 " --> pdb=" O GLU V 48 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 22 Processing helix chain 'W' and resid 35 through 46 removed outlier: 3.625A pdb=" N MET W 40 " --> pdb=" O THR W 36 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA W 41 " --> pdb=" O GLN W 37 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU W 44 " --> pdb=" O MET W 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 22 Processing helix chain 'Y' and resid 23 through 25 No H-bonds generated for 'chain 'Y' and resid 23 through 25' Processing helix chain 'Y' and resid 45 through 54 removed outlier: 3.587A pdb=" N LYS Y 50 " --> pdb=" O VAL Y 46 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL Y 51 " --> pdb=" O GLU Y 47 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE Y 52 " --> pdb=" O PHE Y 48 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG Y 53 " --> pdb=" O ILE Y 49 " (cutoff:3.500A) Processing helix chain '1' and resid 13 through 34 removed outlier: 3.743A pdb=" N ILE 1 18 " --> pdb=" O ILE 1 14 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS 1 19 " --> pdb=" O GLU 1 15 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER 1 20 " --> pdb=" O GLU 1 16 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU 1 28 " --> pdb=" O GLU 1 24 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE 1 30 " --> pdb=" O PHE 1 26 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU 1 32 " --> pdb=" O LEU 1 28 " (cutoff:3.500A) Processing helix chain '1' and resid 41 through 54 removed outlier: 4.344A pdb=" N THR 1 45 " --> pdb=" O ALA 1 41 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG 1 47 " --> pdb=" O ILE 1 43 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE 1 50 " --> pdb=" O VAL 1 46 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG 1 52 " --> pdb=" O LYS 1 48 " (cutoff:3.500A) Processing helix chain '1' and resid 58 through 64 removed outlier: 3.784A pdb=" N GLN 1 64 " --> pdb=" O ARG 1 60 " (cutoff:3.500A) Processing helix chain '2' and resid 23 through 27 Processing helix chain '2' and resid 42 through 48 removed outlier: 3.756A pdb=" N GLN 2 46 " --> pdb=" O ALA 2 42 " (cutoff:3.500A) Processing helix chain '6' and resid 19 through 24 removed outlier: 3.667A pdb=" N SER 6 24 " --> pdb=" O ARG 6 20 " (cutoff:3.500A) Processing helix chain '6' and resid 25 through 39 removed outlier: 3.758A pdb=" N VAL 6 31 " --> pdb=" O ASN 6 27 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU 6 32 " --> pdb=" O GLY 6 28 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG 6 34 " --> pdb=" O LYS 6 30 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG 6 37 " --> pdb=" O ALA 6 33 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 7 removed outlier: 4.012A pdb=" N LEU 9 7 " --> pdb=" O GLN 9 4 " (cutoff:3.500A) Processing helix chain '9' and resid 11 through 17 removed outlier: 3.592A pdb=" N ASP 9 15 " --> pdb=" O VAL 9 11 " (cutoff:3.500A) Processing helix chain '9' and resid 46 through 62 removed outlier: 4.258A pdb=" N ALA 9 50 " --> pdb=" O ARG 9 46 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE 9 51 " --> pdb=" O GLN 9 47 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA 9 52 " --> pdb=" O VAL 9 48 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL 9 55 " --> pdb=" O ILE 9 51 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU 9 57 " --> pdb=" O ARG 9 53 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN 9 62 " --> pdb=" O VAL 9 58 " (cutoff:3.500A) Processing helix chain '9' and resid 93 through 99 Processing helix chain '9' and resid 99 through 104 removed outlier: 3.805A pdb=" N LEU 9 103 " --> pdb=" O ASN 9 99 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR 9 104 " --> pdb=" O ILE 9 100 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 99 through 104' Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'D' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'D' and resid 75 through 81 removed outlier: 4.782A pdb=" N VAL D 77 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 94 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER D 79 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 93 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR D 95 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU D 99 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 116 through 117 removed outlier: 6.715A pdb=" N GLU D 116 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASN D 127 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 162 through 163 removed outlier: 3.565A pdb=" N GLN D 162 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 4 through 16 removed outlier: 5.577A pdb=" N LYS E 9 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU E 29 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY E 11 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL E 27 " --> pdb=" O GLY E 11 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL E 197 " --> pdb=" O THR E 26 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL E 194 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL E 188 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU E 196 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU E 184 " --> pdb=" O LYS E 198 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE E 116 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG E 212 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 34 through 38 removed outlier: 6.982A pdb=" N GLN E 50 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AA9, first strand: chain 'F' and resid 174 through 177 removed outlier: 6.780A pdb=" N VAL F 154 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU F 153 " --> pdb=" O LEU F 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 16 through 20 Processing sheet with id=AB2, first strand: chain 'N' and resid 16 through 24 removed outlier: 7.022A pdb=" N ASN N 45 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL N 19 " --> pdb=" O VAL N 43 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL N 43 " --> pdb=" O VAL N 19 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR N 21 " --> pdb=" O CYS N 41 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N CYS N 41 " --> pdb=" O THR N 21 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS N 23 " --> pdb=" O ILE N 39 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE N 39 " --> pdb=" O LYS N 23 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL N 63 " --> pdb=" O ALA N 83 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA N 83 " --> pdb=" O VAL N 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 70 through 71 removed outlier: 3.698A pdb=" N SER N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR N 76 " --> pdb=" O THR S 75 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL S 70 " --> pdb=" O SER S 67 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR S 60 " --> pdb=" O ARG S 52 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG S 52 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR S 62 " --> pdb=" O ILE S 50 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE S 66 " --> pdb=" O GLU S 46 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N GLU S 46 " --> pdb=" O ILE S 66 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS S 85 " --> pdb=" O HIS S 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 76 through 78 removed outlier: 3.598A pdb=" N ILE O 111 " --> pdb=" O LYS O 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 32 through 34 removed outlier: 3.821A pdb=" N LEU P 34 " --> pdb=" O PHE P 104 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE P 104 " --> pdb=" O LEU P 34 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 41 through 43 removed outlier: 3.746A pdb=" N ILE P 42 " --> pdb=" O ALA P 95 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY P 92 " --> pdb=" O TYR P 74 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR P 72 " --> pdb=" O ILE P 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 29 through 33 removed outlier: 4.674A pdb=" N SER Q 116 " --> pdb=" O GLN Q 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 30 through 31 Processing sheet with id=AB9, first strand: chain 'R' and resid 34 through 35 removed outlier: 4.055A pdb=" N TYR R 34 " --> pdb=" O TYR R 41 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR R 41 " --> pdb=" O TYR R 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'U' and resid 10 through 14 removed outlier: 3.696A pdb=" N ILE U 12 " --> pdb=" O ILE U 5 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE U 40 " --> pdb=" O ILE U 4 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU U 6 " --> pdb=" O VAL U 38 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL U 38 " --> pdb=" O GLU U 6 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 19 through 22 removed outlier: 3.816A pdb=" N ILE U 20 " --> pdb=" O LEU U 95 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE U 97 " --> pdb=" O THR U 61 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR U 61 " --> pdb=" O ILE U 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS U 99 " --> pdb=" O THR U 59 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 71 through 77 removed outlier: 3.678A pdb=" N VAL U 73 " --> pdb=" O LYS U 86 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS U 86 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR U 75 " --> pdb=" O ARG U 84 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG U 84 " --> pdb=" O THR U 75 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER U 82 " --> pdb=" O LYS U 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 2 through 10 removed outlier: 5.519A pdb=" N LYS V 4 " --> pdb=" O VAL V 107 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL V 107 " --> pdb=" O LYS V 4 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL V 6 " --> pdb=" O ILE V 105 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE V 105 " --> pdb=" O VAL V 6 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ARG V 8 " --> pdb=" O ILE V 103 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE V 103 " --> pdb=" O ARG V 8 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N HIS V 102 " --> pdb=" O ALA V 76 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA V 76 " --> pdb=" O HIS V 102 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR V 104 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA V 74 " --> pdb=" O THR V 104 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL V 106 " --> pdb=" O LYS V 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 82 through 87 Processing sheet with id=AC6, first strand: chain 'W' and resid 7 through 10 removed outlier: 6.812A pdb=" N ASP W 28 " --> pdb=" O LYS W 8 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N THR W 26 " --> pdb=" O PRO W 10 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE W 79 " --> pdb=" O VAL W 53 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL W 53 " --> pdb=" O ILE W 79 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N THR W 81 " --> pdb=" O ALA W 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 20 through 21 Processing sheet with id=AC8, first strand: chain 'X' and resid 41 through 42 removed outlier: 4.072A pdb=" N MET X 41 " --> pdb=" O THR X 59 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR X 59 " --> pdb=" O MET X 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'X' and resid 82 through 85 removed outlier: 3.676A pdb=" N ILE X 93 " --> pdb=" O GLY X 82 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Y' and resid 72 through 73 Processing sheet with id=AD2, first strand: chain 'Z' and resid 30 through 31 Processing sheet with id=AD3, first strand: chain 'Z' and resid 38 through 39 removed outlier: 3.637A pdb=" N GLY Z 73 " --> pdb=" O VAL Z 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 43 through 44 removed outlier: 3.706A pdb=" N SER Z 43 " --> pdb=" O ALA Z 69 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Z' and resid 53 through 55 removed outlier: 3.681A pdb=" N VAL Z 87 " --> pdb=" O TYR Z 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '0' and resid 13 through 14 removed outlier: 4.476A pdb=" N THR 0 14 " --> pdb=" O ARG 0 27 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG 0 27 " --> pdb=" O THR 0 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain '2' and resid 3 through 7 removed outlier: 3.531A pdb=" N VAL 2 35 " --> pdb=" O ILE 2 6 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '7' and resid 15 through 16 Processing sheet with id=AD9, first strand: chain '9' and resid 78 through 81 removed outlier: 3.681A pdb=" N ILE 9 80 " --> pdb=" O VAL 9 87 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL 9 86 " --> pdb=" O TYR 9 36 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS 9 88 " --> pdb=" O VAL 9 38 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 909 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 827 hydrogen bonds 1324 hydrogen bond angles 0 basepair planarities 373 basepair parallelities 1309 stacking parallelities Total time for adding SS restraints: 80.96 Time building geometry restraints manager: 34.25 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: 11455 1.33 - 1.45: 36750 1.45 - 1.57: 31746 1.57 - 1.70: 5368 1.70 - 1.82: 89 Bond restraints: 85408 Sorted by residual: bond pdb=" CA ARG D 174 " pdb=" CB ARG D 174 " ideal model delta sigma weight residual 1.526 1.429 0.097 1.76e-02 3.23e+03 3.04e+01 bond pdb=" C1' U A 99 " pdb=" N1 U A 99 " ideal model delta sigma weight residual 1.480 1.557 -0.077 1.50e-02 4.44e+03 2.64e+01 bond pdb=" N PRO D 147 " pdb=" CD PRO D 147 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" CB THR 4 18 " pdb=" CG2 THR 4 18 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.64e+00 bond pdb=" CG ARG O 33 " pdb=" CD ARG O 33 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.84e+00 ... (remaining 85403 not shown) Histogram of bond angle deviations from ideal: 95.69 - 104.36: 10975 104.36 - 113.03: 51731 113.03 - 121.71: 44379 121.71 - 130.38: 20168 130.38 - 139.05: 1343 Bond angle restraints: 128596 Sorted by residual: angle pdb=" CA GLY R 103 " pdb=" C GLY R 103 " pdb=" N ARG R 104 " ideal model delta sigma weight residual 115.43 120.93 -5.50 9.80e-01 1.04e+00 3.15e+01 angle pdb=" C3' U A 661 " pdb=" O3' U A 661 " pdb=" P G A 662 " ideal model delta sigma weight residual 120.20 127.80 -7.60 1.50e+00 4.44e-01 2.57e+01 angle pdb=" C4' U A1750 " pdb=" C3' U A1750 " pdb=" O3' U A1750 " ideal model delta sigma weight residual 109.40 116.26 -6.86 1.50e+00 4.44e-01 2.09e+01 angle pdb=" CA GLY R 103 " pdb=" C GLY R 103 " pdb=" O GLY R 103 " ideal model delta sigma weight residual 121.77 117.84 3.93 8.60e-01 1.35e+00 2.08e+01 angle pdb=" N ILE E 215 " pdb=" CA ILE E 215 " pdb=" C ILE E 215 " ideal model delta sigma weight residual 112.96 108.51 4.45 1.00e+00 1.00e+00 1.98e+01 ... (remaining 128591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 42720 35.53 - 71.07: 2237 71.07 - 106.60: 203 106.60 - 142.14: 26 142.14 - 177.67: 14 Dihedral angle restraints: 45200 sinusoidal: 37790 harmonic: 7410 Sorted by residual: dihedral pdb=" O4' U B 100 " pdb=" C1' U B 100 " pdb=" N1 U B 100 " pdb=" C2 U B 100 " ideal model delta sinusoidal sigma weight residual 200.00 22.92 177.08 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A2384 " pdb=" C1' U A2384 " pdb=" N1 U A2384 " pdb=" C2 U A2384 " ideal model delta sinusoidal sigma weight residual 200.00 24.96 175.04 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C A1932 " pdb=" C1' C A1932 " pdb=" N1 C A1932 " pdb=" C2 C A1932 " ideal model delta sinusoidal sigma weight residual 200.00 26.63 173.37 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 45197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 12565 0.062 - 0.124: 3385 0.124 - 0.186: 545 0.186 - 0.249: 77 0.249 - 0.311: 8 Chirality restraints: 16580 Sorted by residual: chirality pdb=" CG LEU U 25 " pdb=" CB LEU U 25 " pdb=" CD1 LEU U 25 " pdb=" CD2 LEU U 25 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' A A 700 " pdb=" C4' A A 700 " pdb=" O3' A A 700 " pdb=" C2' A A 700 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1' A A 353 " pdb=" O4' A A 353 " pdb=" C2' A A 353 " pdb=" N9 A A 353 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 16577 not shown) Planarity restraints: 6256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 700 " 0.036 2.00e-02 2.50e+03 1.89e-02 9.81e+00 pdb=" N9 A A 700 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A A 700 " -0.011 2.00e-02 2.50e+03 pdb=" N7 A A 700 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A 700 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A A 700 " -0.028 2.00e-02 2.50e+03 pdb=" N6 A A 700 " 0.031 2.00e-02 2.50e+03 pdb=" N1 A A 700 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A A 700 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A A 700 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A A 700 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 557 " 0.038 2.00e-02 2.50e+03 1.74e-02 9.12e+00 pdb=" N9 G A 557 " -0.044 2.00e-02 2.50e+03 pdb=" C8 G A 557 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A 557 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 557 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G A 557 " 0.008 2.00e-02 2.50e+03 pdb=" O6 G A 557 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G A 557 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G A 557 " -0.007 2.00e-02 2.50e+03 pdb=" N2 G A 557 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A 557 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 557 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 845 " -0.035 2.00e-02 2.50e+03 1.71e-02 8.05e+00 pdb=" N9 A A 845 " 0.042 2.00e-02 2.50e+03 pdb=" C8 A A 845 " 0.007 2.00e-02 2.50e+03 pdb=" N7 A A 845 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A A 845 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A A 845 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A A 845 " -0.014 2.00e-02 2.50e+03 pdb=" N1 A A 845 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A 845 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A A 845 " -0.001 2.00e-02 2.50e+03 pdb=" C4 A A 845 " -0.001 2.00e-02 2.50e+03 ... (remaining 6253 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.54: 667 2.54 - 3.19: 62616 3.19 - 3.84: 158154 3.84 - 4.49: 240038 4.49 - 5.14: 324755 Nonbonded interactions: 786230 Sorted by model distance: nonbonded pdb=" O PRO O 48 " pdb=" NZ LYS 7 59 " model vdw 1.886 2.520 nonbonded pdb=" OP2 C A1352 " pdb="MG MG A3006 " model vdw 1.900 2.170 nonbonded pdb=" O2 C A 674 " pdb=" O2' U A 684 " model vdw 1.935 2.440 nonbonded pdb=" OP1 U A2642 " pdb="MG MG A3023 " model vdw 1.961 2.170 nonbonded pdb=" OP1 G A1369 " pdb="MG MG A3006 " model vdw 1.962 2.170 ... (remaining 786225 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 14.420 Check model and map are aligned: 0.860 Set scattering table: 0.550 Process input model: 223.020 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.200 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 245.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.010 0.140 85408 Z= 0.621 Angle : 1.052 14.052 128596 Z= 0.524 Chirality : 0.057 0.311 16580 Planarity : 0.006 0.067 6256 Dihedral : 17.166 177.673 40432 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 17.67 % Favored : 82.18 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -6.09 (0.11), residues: 2553 helix: -4.89 (0.10), residues: 507 sheet: -3.52 (0.21), residues: 353 loop : -4.17 (0.11), residues: 1693 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 519 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 522 average time/residue: 0.8651 time to fit residues: 736.6629 Evaluate side-chains 366 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 3.138 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 439 optimal weight: 3.9990 chunk 394 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 407 optimal weight: 0.9980 chunk 157 optimal weight: 9.9990 chunk 247 optimal weight: 7.9990 chunk 303 optimal weight: 0.6980 chunk 472 optimal weight: 0.0370 overall best weight: 2.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 HIS D 85 ASN D 127 ASN D 142 ASN D 198 GLN E 76 HIS E 143 HIS E 182 ASN F 182 ASN F 188 ASN M 81 HIS Q 97 GLN S 31 HIS S 79 HIS T 37 GLN U 18 GLN U 28 ASN V 61 ASN X 39 ASN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 51 ASN Y 84 ASN Y 88 HIS Z 58 ASN 0 23 ASN 1 27 ASN 7 7 HIS 7 43 GLN 9 63 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 85408 Z= 0.174 Angle : 0.694 9.633 128596 Z= 0.352 Chirality : 0.038 0.274 16580 Planarity : 0.005 0.060 6256 Dihedral : 16.999 176.630 35184 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -5.15 (0.13), residues: 2553 helix: -3.94 (0.15), residues: 526 sheet: -2.85 (0.21), residues: 440 loop : -3.58 (0.12), residues: 1587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 407 time to evaluate : 3.122 Fit side-chains outliers start: 41 outliers final: 27 residues processed: 430 average time/residue: 0.8162 time to fit residues: 593.5764 Evaluate side-chains 373 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 346 time to evaluate : 3.140 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.6182 time to fit residues: 34.8782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 262 optimal weight: 30.0000 chunk 146 optimal weight: 9.9990 chunk 393 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 473 optimal weight: 8.9990 chunk 511 optimal weight: 20.0000 chunk 421 optimal weight: 3.9990 chunk 469 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 379 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 HIS T 44 GLN U 28 ASN U 63 ASN V 61 ASN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 51 ASN Z 58 ASN ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 43 GLN 9 88 HIS 9 91 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.071 85408 Z= 0.420 Angle : 0.922 13.391 128596 Z= 0.455 Chirality : 0.048 0.299 16580 Planarity : 0.007 0.055 6256 Dihedral : 17.631 177.180 35184 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.87 % Favored : 86.09 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -4.82 (0.13), residues: 2553 helix: -3.58 (0.17), residues: 535 sheet: -2.33 (0.24), residues: 424 loop : -3.50 (0.12), residues: 1594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 385 time to evaluate : 3.242 Fit side-chains revert: symmetry clash outliers start: 69 outliers final: 43 residues processed: 430 average time/residue: 0.8187 time to fit residues: 584.4191 Evaluate side-chains 391 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 348 time to evaluate : 3.159 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.5624 time to fit residues: 49.9244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 467 optimal weight: 6.9990 chunk 355 optimal weight: 5.9990 chunk 245 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 317 optimal weight: 4.9990 chunk 474 optimal weight: 10.0000 chunk 502 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 449 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 HIS E 19 ASN ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 HIS O 27 ASN S 14 GLN U 28 ASN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 51 ASN ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 85408 Z= 0.295 Angle : 0.749 11.281 128596 Z= 0.378 Chirality : 0.042 0.273 16580 Planarity : 0.005 0.046 6256 Dihedral : 17.219 178.150 35184 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -4.53 (0.14), residues: 2553 helix: -3.29 (0.17), residues: 551 sheet: -2.09 (0.23), residues: 452 loop : -3.35 (0.13), residues: 1550 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 373 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 44 residues processed: 422 average time/residue: 0.8054 time to fit residues: 570.2548 Evaluate side-chains 393 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 349 time to evaluate : 3.226 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.5808 time to fit residues: 52.2584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 418 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 374 optimal weight: 3.9990 chunk 207 optimal weight: 20.0000 chunk 428 optimal weight: 4.9990 chunk 347 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 256 optimal weight: 10.0000 chunk 451 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 28 ASN ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 85408 Z= 0.245 Angle : 0.681 10.361 128596 Z= 0.346 Chirality : 0.039 0.264 16580 Planarity : 0.005 0.044 6256 Dihedral : 16.897 179.501 35184 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -4.15 (0.14), residues: 2553 helix: -2.92 (0.19), residues: 546 sheet: -1.79 (0.24), residues: 433 loop : -3.13 (0.13), residues: 1574 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 372 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 34 residues processed: 414 average time/residue: 0.8001 time to fit residues: 554.6479 Evaluate side-chains 383 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 349 time to evaluate : 3.234 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.6105 time to fit residues: 42.0357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 169 optimal weight: 30.0000 chunk 452 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 295 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 503 optimal weight: 7.9990 chunk 417 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 264 optimal weight: 30.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 61 ASN U 18 GLN X 51 ASN ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 43 GLN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 85408 Z= 0.390 Angle : 0.850 13.677 128596 Z= 0.421 Chirality : 0.046 0.283 16580 Planarity : 0.006 0.051 6256 Dihedral : 17.287 179.587 35184 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.02 % Favored : 85.98 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -4.27 (0.14), residues: 2553 helix: -3.07 (0.18), residues: 533 sheet: -2.05 (0.23), residues: 461 loop : -3.15 (0.13), residues: 1559 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 356 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 30 residues processed: 387 average time/residue: 0.8704 time to fit residues: 562.1686 Evaluate side-chains 378 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 348 time to evaluate : 3.229 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.6549 time to fit residues: 40.4425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 485 optimal weight: 0.0570 chunk 56 optimal weight: 10.0000 chunk 286 optimal weight: 7.9990 chunk 367 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 423 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 501 optimal weight: 0.8980 chunk 313 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 134 HIS ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 ASN Q 61 ASN U 18 GLN U 28 ASN 1 27 ASN 7 43 GLN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 85408 Z= 0.154 Angle : 0.595 10.562 128596 Z= 0.308 Chirality : 0.036 0.260 16580 Planarity : 0.004 0.041 6256 Dihedral : 16.649 179.062 35184 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -3.85 (0.14), residues: 2553 helix: -2.60 (0.19), residues: 541 sheet: -1.60 (0.25), residues: 422 loop : -2.97 (0.13), residues: 1590 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 376 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 394 average time/residue: 0.8334 time to fit residues: 547.6308 Evaluate side-chains 377 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 359 time to evaluate : 3.206 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.6209 time to fit residues: 24.4156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 310 optimal weight: 6.9990 chunk 200 optimal weight: 30.0000 chunk 299 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 318 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 393 optimal weight: 5.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 61 ASN U 18 GLN X 51 ASN 7 43 GLN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 41 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.068 85408 Z= 0.398 Angle : 0.838 12.898 128596 Z= 0.414 Chirality : 0.046 0.288 16580 Planarity : 0.006 0.050 6256 Dihedral : 17.125 178.887 35184 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.53 % Favored : 85.47 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -4.09 (0.14), residues: 2553 helix: -2.88 (0.18), residues: 542 sheet: -1.89 (0.24), residues: 452 loop : -3.05 (0.13), residues: 1559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 352 time to evaluate : 3.292 Fit side-chains outliers start: 43 outliers final: 29 residues processed: 377 average time/residue: 0.8602 time to fit residues: 541.4494 Evaluate side-chains 373 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 344 time to evaluate : 3.212 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.6204 time to fit residues: 37.6786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 455 optimal weight: 5.9990 chunk 480 optimal weight: 8.9990 chunk 438 optimal weight: 3.9990 chunk 467 optimal weight: 6.9990 chunk 281 optimal weight: 0.3980 chunk 203 optimal weight: 20.0000 chunk 366 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 422 optimal weight: 0.6980 chunk 441 optimal weight: 8.9990 chunk 465 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN U 18 GLN U 28 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 85408 Z= 0.165 Angle : 0.608 10.499 128596 Z= 0.313 Chirality : 0.036 0.255 16580 Planarity : 0.004 0.042 6256 Dihedral : 16.658 178.550 35184 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -3.75 (0.14), residues: 2553 helix: -2.47 (0.20), residues: 543 sheet: -1.61 (0.24), residues: 455 loop : -2.91 (0.13), residues: 1555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 354 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 360 average time/residue: 0.8363 time to fit residues: 503.7675 Evaluate side-chains 349 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 345 time to evaluate : 3.203 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.6848 time to fit residues: 8.1118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 306 optimal weight: 0.4980 chunk 493 optimal weight: 0.0030 chunk 301 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 343 optimal weight: 1.9990 chunk 518 optimal weight: 0.7980 chunk 476 optimal weight: 20.0000 chunk 412 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 318 optimal weight: 0.9990 chunk 252 optimal weight: 10.0000 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 HIS E 19 ASN F 40 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN X 51 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.084 85408 Z= 0.125 Angle : 0.580 11.758 128596 Z= 0.300 Chirality : 0.034 0.266 16580 Planarity : 0.004 0.058 6256 Dihedral : 16.569 178.707 35184 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.62 % Favored : 91.34 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -3.51 (0.15), residues: 2553 helix: -2.23 (0.20), residues: 544 sheet: -1.45 (0.25), residues: 446 loop : -2.77 (0.13), residues: 1563 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 352 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 354 average time/residue: 0.8458 time to fit residues: 502.0467 Evaluate side-chains 348 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 343 time to evaluate : 3.290 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.7174 time to fit residues: 9.9998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 327 optimal weight: 0.0270 chunk 439 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 380 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 413 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 424 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 overall best weight: 6.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN U 18 GLN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.169255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146294 restraints weight = 126303.521| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.36 r_work: 0.3501 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 85408 Z= 0.325 Angle : 0.758 11.564 128596 Z= 0.377 Chirality : 0.042 0.274 16580 Planarity : 0.005 0.043 6256 Dihedral : 16.867 177.060 35184 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -3.73 (0.14), residues: 2553 helix: -2.49 (0.19), residues: 545 sheet: -1.58 (0.25), residues: 445 loop : -2.89 (0.13), residues: 1563 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11023.99 seconds wall clock time: 198 minutes 30.81 seconds (11910.81 seconds total)