Starting phenix.real_space_refine (version: dev) on Wed Feb 22 10:07:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/02_2023/5lmt_4079_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/02_2023/5lmt_4079.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/02_2023/5lmt_4079_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/02_2023/5lmt_4079_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/02_2023/5lmt_4079_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/02_2023/5lmt_4079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/02_2023/5lmt_4079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/02_2023/5lmt_4079_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/02_2023/5lmt_4079_neut_updated.pdb" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.024 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 Process input model Symmetric amino acids flipped Residue "B GLU 9": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E GLU 8": "OE1" <-> "OE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 149": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G ARG 79": "NH1" <-> "NH2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I GLU 2": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "L GLU 16": "OE1" <-> "OE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O GLU 7": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 54": "OE1" <-> "OE2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 78": "OE1" <-> "OE2" Residue "Q GLU 86": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 38": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "T GLU 50": "OE1" <-> "OE2" Residue "T GLU 51": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "W GLU 15": "OE1" <-> "OE2" Residue "W GLU 31": "OE1" <-> "OE2" Residue "X GLU 84": "OE1" <-> "OE2" Residue "X ARG 123": "NH1" <-> "NH2" Residue "X ARG 125": "NH1" <-> "NH2" Residue "X GLU 126": "OE1" <-> "OE2" Residue "X GLU 131": "OE1" <-> "OE2" Residue "X GLU 155": "OE1" <-> "OE2" Residue "X ARG 159": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 55776 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 32544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1515, 32544 Inner-chain residues flagged as termini: ['pdbres=" G A 567 "', 'pdbres=" C A1397 "'] Classifications: {'RNA': 1515} Modifications used: {'5*END': 3, 'rna2p_pur': 105, 'rna2p_pyr': 71, 'rna3p_pur': 750, 'rna3p_pyr': 589} Link IDs: {'rna2p': 176, 'rna3p': 1338} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 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: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} 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: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 885 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} 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: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 946 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} 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: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 655 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1336 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 1 Chain: "Y" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 439 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 14, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 17} Chain breaks: 2 Chain: "Z" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p': 5, 'rna3p_pur': 33, 'rna3p_pyr': 28} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Unusual residues: {' MG': 83} Classifications: {'undetermined': 83} Link IDs: {None: 82} 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: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36115 SG CYS D 9 85.508 103.328 147.726 1.00 50.00 S ATOM 36258 SG CYS D 26 82.742 104.738 147.843 1.00 50.00 S ATOM 36298 SG CYS D 31 84.963 106.198 147.107 1.00 50.00 S ATOM 46915 SG CYS N 24 148.406 114.012 137.443 1.00 50.00 S ATOM 46939 SG CYS N 27 146.439 111.490 136.408 1.00 50.00 S ATOM 47071 SG CYS N 43 145.217 114.380 135.008 1.00 50.00 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="ZN ZN N 101 " occ=0.92 residue: pdb="MG MG W 101 " occ=0.63 Time building chain proxies: 23.48, per 1000 atoms: 0.42 Number of scatterers: 55776 At special positions: 0 Unit cell: (225.12, 176.88, 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 61 16.00 P 1609 15.00 Mg 86 11.99 O 14846 8.00 N 10490 7.00 C 28682 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: 25.24 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 300 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 31 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 9 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 26 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4838 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 24 sheets defined 33.8% alpha, 15.2% beta 523 base pairs and 916 stacking pairs defined. Time for finding SS restraints: 21.35 Creating SS restraints... Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 44 through 62 Processing helix chain 'B' and resid 77 through 87 removed outlier: 4.467A pdb=" N ARG B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 121 removed outlier: 4.019A pdb=" N GLN B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 148 removed outlier: 3.593A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 179 Processing helix chain 'B' and resid 208 through 226 removed outlier: 3.845A pdb=" N ILE B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 10 No H-bonds generated for 'chain 'C' and resid 7 through 10' Processing helix chain 'C' and resid 29 through 47 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 53 through 68 removed outlier: 3.548A pdb=" N ARG D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 84 Processing helix chain 'D' and resid 89 through 98 Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 114 through 122 Processing helix chain 'D' and resid 156 through 165 Processing helix chain 'D' and resid 200 through 208 Processing helix chain 'E' and resid 51 through 64 Processing helix chain 'E' and resid 104 through 113 Processing helix chain 'E' and resid 128 through 141 Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'F' and resid 17 through 32 Processing helix chain 'F' and resid 69 through 81 removed outlier: 5.047A pdb=" N ASN F 73 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP F 74 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 53 Processing helix chain 'G' and resid 58 through 69 Processing helix chain 'G' and resid 93 through 110 Processing helix chain 'G' and resid 116 through 129 Processing helix chain 'G' and resid 134 through 147 Processing helix chain 'G' and resid 151 through 153 No H-bonds generated for 'chain 'G' and resid 151 through 153' Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 103 through 106 Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'I' and resid 33 through 36 No H-bonds generated for 'chain 'I' and resid 33 through 36' Processing helix chain 'I' and resid 42 through 45 Processing helix chain 'I' and resid 48 through 52 Processing helix chain 'I' and resid 70 through 88 Processing helix chain 'I' and resid 92 through 95 Processing helix chain 'J' and resid 13 through 28 removed outlier: 3.731A pdb=" N ILE J 23 " --> pdb=" O SER J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 87 removed outlier: 4.537A pdb=" N MET J 86 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR J 87 " --> pdb=" O GLU J 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 48 No H-bonds generated for 'chain 'K' and resid 46 through 48' Processing helix chain 'K' and resid 53 through 56 removed outlier: 3.982A pdb=" N GLY K 56 " --> pdb=" O SER K 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 53 through 56' Processing helix chain 'K' and resid 58 through 75 removed outlier: 3.659A pdb=" N TYR K 75 " --> pdb=" O LYS K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 101 Processing helix chain 'L' and resid 7 through 13 Processing helix chain 'M' and resid 15 through 21 removed outlier: 3.625A pdb=" N TYR M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 37 removed outlier: 3.578A pdb=" N LYS M 31 " --> pdb=" O LYS M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 61 Processing helix chain 'M' and resid 67 through 83 Processing helix chain 'M' and resid 87 through 94 Processing helix chain 'N' and resid 4 through 6 No H-bonds generated for 'chain 'N' and resid 4 through 6' Processing helix chain 'N' and resid 17 through 19 No H-bonds generated for 'chain 'N' and resid 17 through 19' Processing helix chain 'N' and resid 41 through 50 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 Processing helix chain 'O' and resid 51 through 73 removed outlier: 3.716A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 85 Processing helix chain 'P' and resid 53 through 62 Processing helix chain 'P' and resid 68 through 76 Processing helix chain 'Q' and resid 82 through 97 removed outlier: 3.603A pdb=" N LYS Q 87 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 56 No H-bonds generated for 'chain 'R' and resid 53 through 56' Processing helix chain 'R' and resid 60 through 76 Processing helix chain 'S' and resid 16 through 19 No H-bonds generated for 'chain 'S' and resid 16 through 19' Processing helix chain 'S' and resid 71 through 73 No H-bonds generated for 'chain 'S' and resid 71 through 73' Processing helix chain 'T' and resid 13 through 45 Processing helix chain 'T' and resid 50 through 68 Processing helix chain 'T' and resid 74 through 93 removed outlier: 3.597A pdb=" N ALA T 78 " --> pdb=" O LYS T 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 15 Processing helix chain 'W' and resid 38 through 43 Processing helix chain 'X' and resid 31 through 41 Processing helix chain 'X' and resid 62 through 76 Processing helix chain 'X' and resid 96 through 112 Processing helix chain 'X' and resid 130 through 143 removed outlier: 3.549A pdb=" N ARG X 139 " --> pdb=" O ARG X 135 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 68 through 71 removed outlier: 6.874A pdb=" N ALA B 161 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL B 71 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE B 163 " --> pdb=" O VAL B 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 32 through 35 removed outlier: 6.988A pdb=" N ILE B 41 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 55 through 59 Processing sheet with id= D, first strand: chain 'C' and resid 169 through 171 Processing sheet with id= E, first strand: chain 'D' and resid 126 through 128 Processing sheet with id= F, first strand: chain 'E' and resid 66 through 68 removed outlier: 5.874A pdb=" N VAL E 33 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N MET E 10 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY E 35 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU E 8 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 80 through 84 Processing sheet with id= H, first strand: chain 'F' and resid 44 through 47 removed outlier: 4.092A pdb=" N GLY F 44 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG F 2 " --> pdb=" O MET F 67 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 35 through 41 removed outlier: 6.634A pdb=" N GLN F 64 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N VAL F 40 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TRP F 62 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 73 through 80 Processing sheet with id= K, first strand: chain 'H' and resid 82 through 84 removed outlier: 6.966A pdb=" N ILE H 111 " --> pdb=" O ILE H 134 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU H 136 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE H 109 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 45 through 49 removed outlier: 6.801A pdb=" N TYR H 62 " --> pdb=" O LYS H 46 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR H 48 " --> pdb=" O ARG H 60 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG H 60 " --> pdb=" O TYR H 48 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.798A pdb=" N ARG I 20 " --> pdb=" O ASP I 60 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 94 through 99 removed outlier: 4.466A pdb=" N ASN J 69 " --> pdb=" O LEU J 40 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 43 through 50 removed outlier: 3.635A pdb=" N VAL J 49 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU J 61 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'K' and resid 39 through 43 removed outlier: 6.857A pdb=" N ILE K 32 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TRP K 42 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL K 30 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER K 79 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA K 19 " --> pdb=" O SER K 79 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASP K 81 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE K 21 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE K 83 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ALA K 23 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG K 85 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'L' and resid 82 through 85 removed outlier: 6.797A pdb=" N LYS L 57 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL L 40 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL L 55 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR L 42 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG L 53 " --> pdb=" O THR L 42 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'P' and resid 2 through 8 removed outlier: 6.513A pdb=" N VAL P 21 " --> pdb=" O LYS P 35 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LYS P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Q' and resid 71 through 73 removed outlier: 14.187A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.253A pdb=" N GLN Q 26 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N THR Q 7 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU Q 24 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR Q 20 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'Q' and resid 56 through 58 removed outlier: 5.935A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU Q 76 " --> pdb=" O GLU Q 58 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'S' and resid 31 through 33 Processing sheet with id= V, first strand: chain 'W' and resid 52 through 57 removed outlier: 3.576A pdb=" N THR W 9 " --> pdb=" O VAL W 55 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG W 23 " --> pdb=" O THR W 14 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA W 16 " --> pdb=" O THR W 21 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N THR W 21 " --> pdb=" O ALA W 16 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE W 32 " --> pdb=" O VAL W 24 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 25 through 30 removed outlier: 6.254A pdb=" N VAL X 18 " --> pdb=" O LEU X 26 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE X 28 " --> pdb=" O VAL X 16 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL X 16 " --> pdb=" O ILE X 28 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG X 58 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU X 47 " --> pdb=" O ARG X 58 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 85 through 90 removed outlier: 6.439A pdb=" N LYS X 115 " --> pdb=" O LYS X 86 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE X 88 " --> pdb=" O LYS X 115 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS X 117 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N PHE X 90 " --> pdb=" O LYS X 117 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR X 119 " --> pdb=" O PHE X 90 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA X 166 " --> pdb=" O VAL X 150 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL X 150 " --> pdb=" O ALA X 166 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1398 hydrogen bonds 2382 hydrogen bond angles 0 basepair planarities 523 basepair parallelities 916 stacking parallelities Total time for adding SS restraints: 40.51 Time building geometry restraints manager: 26.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11678 1.34 - 1.46: 23653 1.46 - 1.59: 21595 1.59 - 1.71: 3108 1.71 - 1.84: 107 Bond restraints: 60141 Sorted by residual: bond pdb=" C4 5MU Z 54 " pdb=" C5 5MU Z 54 " ideal model delta sigma weight residual 1.802 1.499 0.303 2.00e-02 2.50e+03 2.30e+02 bond pdb=" N1 5MU Z 54 " pdb=" C6 5MU Z 54 " ideal model delta sigma weight residual 1.635 1.358 0.277 2.00e-02 2.50e+03 1.91e+02 bond pdb=" C5 5MU Z 54 " pdb=" C6 5MU Z 54 " ideal model delta sigma weight residual 1.155 1.404 -0.249 2.00e-02 2.50e+03 1.56e+02 bond pdb=" N3 5MU Z 54 " pdb=" C4 5MU Z 54 " ideal model delta sigma weight residual 1.182 1.344 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" C2 4SU Z 8 " pdb=" N3 4SU Z 8 " ideal model delta sigma weight residual 1.498 1.349 0.149 2.00e-02 2.50e+03 5.57e+01 ... (remaining 60136 not shown) Histogram of bond angle deviations from ideal: 78.91 - 90.62: 3 90.62 - 102.33: 2569 102.33 - 114.04: 42018 114.04 - 125.75: 38388 125.75 - 137.46: 6166 Bond angle restraints: 89144 Sorted by residual: angle pdb=" C THR I 7 " pdb=" CA THR I 7 " pdb=" CB THR I 7 " ideal model delta sigma weight residual 111.22 78.91 32.31 1.72e+00 3.38e-01 3.53e+02 angle pdb=" N ARG E 15 " pdb=" CA ARG E 15 " pdb=" C ARG E 15 " ideal model delta sigma weight residual 109.46 78.97 30.49 1.66e+00 3.63e-01 3.37e+02 angle pdb=" N ARG W 23 " pdb=" CA ARG W 23 " pdb=" C ARG W 23 " ideal model delta sigma weight residual 109.76 83.88 25.88 1.59e+00 3.96e-01 2.65e+02 angle pdb=" O3' G A 575 " pdb=" C3' G A 575 " pdb=" C2' G A 575 " ideal model delta sigma weight residual 109.50 127.98 -18.48 1.50e+00 4.44e-01 1.52e+02 angle pdb=" N ARG D 36 " pdb=" CA ARG D 36 " pdb=" C ARG D 36 " ideal model delta sigma weight residual 109.81 136.45 -26.64 2.21e+00 2.05e-01 1.45e+02 ... (remaining 89139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 30259 35.94 - 71.87: 2130 71.87 - 107.81: 176 107.81 - 143.74: 23 143.74 - 179.68: 52 Dihedral angle restraints: 32640 sinusoidal: 25113 harmonic: 7527 Sorted by residual: dihedral pdb=" C THR I 7 " pdb=" N THR I 7 " pdb=" CA THR I 7 " pdb=" CB THR I 7 " ideal model delta harmonic sigma weight residual -122.00 -84.53 -37.47 0 2.50e+00 1.60e-01 2.25e+02 dihedral pdb=" C ARG E 15 " pdb=" N ARG E 15 " pdb=" CA ARG E 15 " pdb=" CB ARG E 15 " ideal model delta harmonic sigma weight residual -122.60 -89.53 -33.07 0 2.50e+00 1.60e-01 1.75e+02 dihedral pdb=" C5' A A 559 " pdb=" C4' A A 559 " pdb=" C3' A A 559 " pdb=" O3' A A 559 " ideal model delta sinusoidal sigma weight residual 147.00 67.56 79.44 1 8.00e+00 1.56e-02 1.22e+02 ... (remaining 32637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.250: 10766 0.250 - 0.501: 365 0.501 - 0.751: 31 0.751 - 1.002: 6 1.002 - 1.252: 4 Chirality restraints: 11172 Sorted by residual: 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 -1.49 -1.25 2.00e-01 2.50e+01 3.92e+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 -1.68 -1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" C3' C A 328 " pdb=" C4' C A 328 " pdb=" O3' C A 328 " pdb=" C2' C A 328 " both_signs ideal model delta sigma weight residual False -2.74 -1.73 -1.02 2.00e-01 2.50e+01 2.60e+01 ... (remaining 11169 not shown) Planarity restraints: 5328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC Z 32 " -0.013 2.00e-02 2.50e+03 5.36e-01 6.45e+03 pdb=" C4' OMC Z 32 " -0.415 2.00e-02 2.50e+03 pdb=" O4' OMC Z 32 " -0.511 2.00e-02 2.50e+03 pdb=" C3' OMC Z 32 " 0.580 2.00e-02 2.50e+03 pdb=" O3' OMC Z 32 " 0.535 2.00e-02 2.50e+03 pdb=" C2' OMC Z 32 " 0.189 2.00e-02 2.50e+03 pdb=" O2' OMC Z 32 " -0.894 2.00e-02 2.50e+03 pdb=" C1' OMC Z 32 " -0.260 2.00e-02 2.50e+03 pdb=" N1 OMC Z 32 " 0.789 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU Z 54 " 0.289 2.00e-02 2.50e+03 4.43e-01 4.42e+03 pdb=" C4' 5MU Z 54 " -0.375 2.00e-02 2.50e+03 pdb=" O4' 5MU Z 54 " -0.739 2.00e-02 2.50e+03 pdb=" C3' 5MU Z 54 " 0.481 2.00e-02 2.50e+03 pdb=" O3' 5MU Z 54 " 0.064 2.00e-02 2.50e+03 pdb=" C2' 5MU Z 54 " 0.362 2.00e-02 2.50e+03 pdb=" O2' 5MU Z 54 " -0.393 2.00e-02 2.50e+03 pdb=" C1' 5MU Z 54 " -0.308 2.00e-02 2.50e+03 pdb=" N1 5MU Z 54 " 0.619 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' G7M Z 46 " -0.060 2.00e-02 2.50e+03 4.17e-01 3.92e+03 pdb=" C4' G7M Z 46 " -0.364 2.00e-02 2.50e+03 pdb=" O4' G7M Z 46 " -0.269 2.00e-02 2.50e+03 pdb=" C3' G7M Z 46 " 0.538 2.00e-02 2.50e+03 pdb=" O3' G7M Z 46 " 0.337 2.00e-02 2.50e+03 pdb=" C2' G7M Z 46 " 0.274 2.00e-02 2.50e+03 pdb=" O2' G7M Z 46 " -0.732 2.00e-02 2.50e+03 pdb=" C1' G7M Z 46 " -0.253 2.00e-02 2.50e+03 pdb=" N9 G7M Z 46 " 0.529 2.00e-02 2.50e+03 ... (remaining 5325 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 31 2.01 - 2.73: 5660 2.73 - 3.46: 80192 3.46 - 4.18: 187550 4.18 - 4.90: 247772 Nonbonded interactions: 521205 Sorted by model distance: nonbonded pdb=" OP1 G A1508 " pdb="MG MG A1608 " model vdw 1.290 2.170 nonbonded pdb=" NZ LYS C 26 " pdb=" NE ARG J 45 " model vdw 1.369 3.200 nonbonded pdb=" OP1 G A 558 " pdb="MG MG A1678 " model vdw 1.380 2.170 nonbonded pdb=" OP1 C A 578 " pdb="MG MG A1674 " model vdw 1.424 2.170 nonbonded pdb=" OP2 A A 195 " pdb="MG MG A1609 " model vdw 1.472 2.170 ... (remaining 521200 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1609 5.49 5 Mg 86 5.21 5 S 61 5.16 5 C 28682 2.51 5 N 10490 2.21 5 O 14846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.63 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: 0.650 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: 0.030 Extract box with map and model: 7.790 Check model and map are aligned: 0.650 Process input model: 159.080 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.410 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 : 0.008 0.303 60141 Z= 0.526 Angle : 1.431 32.310 89144 Z= 0.956 Chirality : 0.120 1.252 11172 Planarity : 0.016 0.536 5328 Dihedral : 20.755 179.678 27802 Min Nonbonded Distance : 1.290 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 3.30 % Allowed : 11.92 % Favored : 84.78 % Rotamer Outliers : 22.35 % Cbeta Deviations : 0.87 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.08 % 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: -2.73 (0.14), residues: 2576 helix: 0.09 (0.14), residues: 1006 sheet: -2.07 (0.25), residues: 364 loop : -3.54 (0.14), residues: 1206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1493 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 491 poor density : 1002 time to evaluate : 2.943 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: 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: 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 outliers start: 491 outliers final: 106 residues processed: 1262 average time/residue: 0.6836 time to fit residues: 1340.4535 Evaluate side-chains 748 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 642 time to evaluate : 2.897 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 3 residues processed: 106 average time/residue: 0.6169 time to fit residues: 110.7107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 347 optimal weight: 6.9990 chunk 311 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 322 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 195 optimal weight: 7.9990 chunk 239 optimal weight: 30.0000 chunk 373 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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** ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN E 73 ASN F 18 GLN G 37 ASN G 86 GLN ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 HIS H 15 ASN H 78 GLN I 31 GLN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN J 56 HIS J 76 ASN J 78 ASN K 22 HIS ** K 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN L 49 ASN M 92 HIS ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 HIS W 19 ASN ** X 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 60141 Z= 0.353 Angle : 0.912 15.514 89144 Z= 0.477 Chirality : 0.048 0.385 11172 Planarity : 0.008 0.123 5328 Dihedral : 17.523 179.926 22319 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 29.88 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.93 % Favored : 90.37 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.16 % 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: -1.75 (0.16), residues: 2576 helix: 0.93 (0.16), residues: 989 sheet: -1.73 (0.24), residues: 402 loop : -2.90 (0.15), residues: 1185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 810 time to evaluate : 2.870 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: 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 outliers start: 14 outliers final: 5 residues processed: 820 average time/residue: 0.6047 time to fit residues: 800.5554 Evaluate side-chains 589 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 584 time to evaluate : 2.900 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4008 time to fit residues: 6.9303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 207 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 310 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 373 optimal weight: 5.9990 chunk 403 optimal weight: 20.0000 chunk 332 optimal weight: 20.0000 chunk 370 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 299 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN D 103 ASN D 201 GLN E 56 GLN E 73 ASN ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 GLN ** M 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 26 ASN ** X 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 60141 Z= 0.257 Angle : 0.764 14.802 89144 Z= 0.405 Chirality : 0.041 0.332 11172 Planarity : 0.007 0.128 5328 Dihedral : 16.827 179.153 22319 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 24.77 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.81 % Favored : 90.61 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.08 % 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: -1.62 (0.16), residues: 2576 helix: 0.75 (0.16), residues: 987 sheet: -1.75 (0.23), residues: 423 loop : -2.49 (0.16), residues: 1166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 747 time to evaluate : 3.089 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: 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 outliers start: 8 outliers final: 3 residues processed: 751 average time/residue: 0.5957 time to fit residues: 726.6983 Evaluate side-chains 572 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 569 time to evaluate : 2.877 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4681 time to fit residues: 5.6547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 369 optimal weight: 3.9990 chunk 281 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 251 optimal weight: 9.9990 chunk 375 optimal weight: 3.9990 chunk 397 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 355 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 HIS T 26 ASN ** X 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 60141 Z= 0.288 Angle : 0.766 14.571 89144 Z= 0.403 Chirality : 0.041 0.316 11172 Planarity : 0.007 0.129 5328 Dihedral : 16.648 178.727 22319 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 27.50 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.12 % Favored : 90.33 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.08 % 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: -1.63 (0.16), residues: 2576 helix: 0.62 (0.16), residues: 960 sheet: -1.78 (0.22), residues: 440 loop : -2.28 (0.17), residues: 1176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 700 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 701 average time/residue: 0.5866 time to fit residues: 674.5412 Evaluate side-chains 544 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 544 time to evaluate : 2.899 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 330 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 295 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 339 optimal weight: 6.9990 chunk 274 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 202 optimal weight: 20.0000 chunk 356 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN G 97 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 26 ASN ** X 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 60141 Z= 0.215 Angle : 0.709 14.401 89144 Z= 0.375 Chirality : 0.038 0.315 11172 Planarity : 0.006 0.131 5328 Dihedral : 16.426 179.490 22319 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 24.84 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.11 % Favored : 91.46 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -1.45 (0.16), residues: 2576 helix: 0.67 (0.17), residues: 960 sheet: -1.62 (0.23), residues: 432 loop : -2.10 (0.17), residues: 1184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 700 time to evaluate : 2.968 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: 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 outliers start: 2 outliers final: 0 residues processed: 701 average time/residue: 0.5907 time to fit residues: 677.5898 Evaluate side-chains 559 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 559 time to evaluate : 2.905 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 133 optimal weight: 10.0000 chunk 357 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 233 optimal weight: 30.0000 chunk 98 optimal weight: 20.0000 chunk 397 optimal weight: 20.0000 chunk 330 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 208 optimal weight: 20.0000 overall best weight: 13.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN B 113 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN D 103 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN F 94 GLN G 86 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 ASN W 43 HIS ** X 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.128 60141 Z= 0.581 Angle : 1.040 14.503 89144 Z= 0.528 Chirality : 0.051 0.432 11172 Planarity : 0.009 0.129 5328 Dihedral : 17.445 179.311 22319 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 46.68 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.65 % Favored : 87.89 % Rotamer Outliers : 0.14 % 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: -2.35 (0.16), residues: 2576 helix: -0.54 (0.15), residues: 982 sheet: -1.78 (0.24), residues: 398 loop : -2.34 (0.17), residues: 1196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 607 time to evaluate : 2.955 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: symmetry clash outliers start: 3 outliers final: 1 residues processed: 609 average time/residue: 0.5910 time to fit residues: 593.4922 Evaluate side-chains 491 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 490 time to evaluate : 2.887 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4782 time to fit residues: 4.0150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 383 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 334 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 396 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN D 103 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN ** X 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 60141 Z= 0.256 Angle : 0.771 15.951 89144 Z= 0.405 Chirality : 0.040 0.316 11172 Planarity : 0.007 0.130 5328 Dihedral : 16.879 179.666 22319 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 28.28 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.58 % Favored : 90.99 % Rotamer Outliers : 0.00 % 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: -1.86 (0.16), residues: 2576 helix: -0.04 (0.16), residues: 973 sheet: -1.58 (0.24), residues: 407 loop : -2.12 (0.17), residues: 1196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 651 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 0 outliers final: 0 residues processed: 651 average time/residue: 0.6135 time to fit residues: 655.5095 Evaluate side-chains 517 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 517 time to evaluate : 2.876 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 245 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 269 optimal weight: 8.9990 chunk 195 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 311 optimal weight: 0.0370 overall best weight: 6.0066 ------------------------------------------------------------------------------- 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 104 ASN B 113 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS J 76 ASN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 162 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 60141 Z= 0.298 Angle : 0.776 13.979 89144 Z= 0.407 Chirality : 0.040 0.307 11172 Planarity : 0.007 0.129 5328 Dihedral : 16.751 179.414 22319 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 30.82 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.82 % Favored : 89.75 % Rotamer Outliers : 0.00 % 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: -1.88 (0.16), residues: 2576 helix: -0.10 (0.16), residues: 983 sheet: -1.48 (0.24), residues: 429 loop : -2.16 (0.18), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 628 time to evaluate : 2.928 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 628 average time/residue: 0.5872 time to fit residues: 610.0271 Evaluate side-chains 502 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 2.926 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 360 optimal weight: 6.9990 chunk 379 optimal weight: 7.9990 chunk 346 optimal weight: 6.9990 chunk 369 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 289 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 333 optimal weight: 0.9980 chunk 349 optimal weight: 5.9990 chunk 367 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 HIS ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN K 116 HIS ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 HIS ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 60141 Z= 0.200 Angle : 0.715 13.716 89144 Z= 0.376 Chirality : 0.037 0.295 11172 Planarity : 0.006 0.130 5328 Dihedral : 16.416 179.682 22319 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 24.77 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.88 % Favored : 91.69 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.16), residues: 2576 helix: 0.05 (0.16), residues: 982 sheet: -1.43 (0.24), residues: 430 loop : -2.04 (0.18), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 time to evaluate : 3.063 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 0.5867 time to fit residues: 645.0624 Evaluate side-chains 511 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 511 time to evaluate : 4.009 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 242 optimal weight: 0.9990 chunk 390 optimal weight: 20.0000 chunk 238 optimal weight: 0.0980 chunk 185 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 409 optimal weight: 30.0000 chunk 376 optimal weight: 4.9990 chunk 326 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 251 optimal weight: 8.9990 chunk 199 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN G 86 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS J 21 GLN ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 HIS Q 16 GLN S 14 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.087 60141 Z= 0.172 Angle : 0.695 13.661 89144 Z= 0.365 Chirality : 0.036 0.312 11172 Planarity : 0.007 0.130 5328 Dihedral : 16.151 179.660 22319 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.92 % Favored : 91.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.16), residues: 2576 helix: 0.15 (0.16), residues: 966 sheet: -1.42 (0.24), residues: 436 loop : -1.93 (0.18), residues: 1174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 672 time to evaluate : 2.898 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 0.5909 time to fit residues: 654.2884 Evaluate side-chains 518 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 518 time to evaluate : 2.919 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 258 optimal weight: 4.9990 chunk 347 optimal weight: 9.9990 chunk 99 optimal weight: 30.0000 chunk 300 optimal weight: 0.2980 chunk 48 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 326 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 335 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN G 86 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 HIS S 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.066762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.055838 restraints weight = 293806.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.057420 restraints weight = 117885.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.058197 restraints weight = 65450.879| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.6455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 60141 Z= 0.255 Angle : 0.730 13.559 89144 Z= 0.383 Chirality : 0.038 0.308 11172 Planarity : 0.007 0.129 5328 Dihedral : 16.232 179.273 22319 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 27.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.85 % Favored : 90.84 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.16), residues: 2576 helix: 0.04 (0.16), residues: 980 sheet: -1.33 (0.24), residues: 421 loop : -1.88 (0.18), residues: 1175 =============================================================================== Job complete usr+sys time: 10841.02 seconds wall clock time: 193 minutes 35.28 seconds (11615.28 seconds total)