Starting phenix.real_space_refine (version: dev) on Thu May 12 20:47:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/05_2022/5lmt_4079_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/05_2022/5lmt_4079.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/05_2022/5lmt_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_4079/05_2022/5lmt_4079_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/05_2022/5lmt_4079_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/05_2022/5lmt_4079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/05_2022/5lmt_4079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/05_2022/5lmt_4079_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmt_4079/05_2022/5lmt_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 Convert atoms to be neutral 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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, 'rna3p_pur': 750, 'rna2p_pyr': 71, 'rna3p_pyr': 589} Link IDs: {'rna3p': 1338, 'rna2p': 176} 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: {'rna3p_pyr': 3, 'rna2p_pur': 2, 'rna3p_pur': 14, 'rna2p_pyr': 1} Link IDs: {'rna3p': 17, 'rna2p': 2} 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: {'rna3p_pyr': 28, 'rna2p_pur': 5, 'rna3p_pur': 33, 'rna2p_pyr': 6, 'rna3p': 5} Link IDs: {'rna3p': 65, 'rna2p': 11} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 2 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: 25.88, per 1000 atoms: 0.46 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: 22.84 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral 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: 23.09 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: 41.33 Time building geometry restraints manager: 24.68 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 1.805 1.499 0.306 2.00e-02 2.50e+03 2.35e+02 bond pdb=" N1 5MU Z 54 " pdb=" C6 5MU Z 54 " ideal model delta sigma weight residual 1.638 1.358 0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C5 5MU Z 54 " pdb=" C6 5MU Z 54 " ideal model delta sigma weight residual 1.150 1.404 -0.254 2.00e-02 2.50e+03 1.62e+02 bond pdb=" N3 5MU Z 54 " pdb=" C4 5MU Z 54 " ideal model delta sigma weight residual 1.179 1.344 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" C2 4SU Z 8 " pdb=" N3 4SU Z 8 " ideal model delta sigma weight residual 1.497 1.349 0.148 2.00e-02 2.50e+03 5.49e+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: 30248 35.94 - 71.87: 2127 71.87 - 107.81: 174 107.81 - 143.74: 23 143.74 - 179.68: 52 Dihedral angle restraints: 32624 sinusoidal: 25097 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 32621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.250: 10774 0.250 - 0.501: 365 0.501 - 0.751: 31 0.751 - 1.002: 6 1.002 - 1.252: 4 Chirality restraints: 11180 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 11177 not shown) Planarity restraints: 5326 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=" C1' C A 71 " -0.046 2.00e-02 2.50e+03 6.21e-02 8.68e+01 pdb=" N1 C A 71 " 0.002 2.00e-02 2.50e+03 pdb=" C2 C A 71 " 0.090 2.00e-02 2.50e+03 pdb=" O2 C A 71 " -0.064 2.00e-02 2.50e+03 pdb=" N3 C A 71 " 0.043 2.00e-02 2.50e+03 pdb=" C4 C A 71 " 0.081 2.00e-02 2.50e+03 pdb=" N4 C A 71 " -0.110 2.00e-02 2.50e+03 pdb=" C5 C A 71 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C A 71 " 0.001 2.00e-02 2.50e+03 ... (remaining 5323 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.640 Check model and map are aligned: 0.640 Convert atoms to be neutral: 0.400 Process input model: 161.290 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.390 ------------------------------------------------------------------------------- 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 0.306 60141 Z= 0.527 Angle : 1.430 32.310 89144 Z= 0.956 Chirality : 0.120 1.252 11180 Planarity : 0.014 0.536 5326 Dihedral : 20.735 179.678 27786 Min Nonbonded Distance : 1.290 Molprobity Statistics. All-atom Clashscore : 18.82 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 : 2.952 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 revert: symmetry clash outliers start: 491 outliers final: 106 residues processed: 1262 average time/residue: 0.6456 time to fit residues: 1263.0659 Evaluate side-chains 747 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 641 time to evaluate : 2.843 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: 0.6013 time to fit residues: 107.9052 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 13 GLN 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: 0.7636 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.109 60141 Z= 0.352 Angle : 0.885 14.667 89144 Z= 0.466 Chirality : 0.048 0.403 11180 Planarity : 0.007 0.124 5326 Dihedral : 17.501 178.796 22303 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 29.07 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.67 % Favored : 89.64 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.20 % 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: -1.78 (0.16), residues: 2576 helix: 0.87 (0.16), residues: 993 sheet: -1.71 (0.24), residues: 405 loop : -2.91 (0.15), residues: 1178 *********************** 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 825 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 811 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 4 residues processed: 818 average time/residue: 0.5824 time to fit residues: 769.4564 Evaluate side-chains 592 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 588 time to evaluate : 2.891 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3788 time to fit residues: 6.0313 ------------------------------------------------------------------------------- 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: 3.9990 chunk 254 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 373 optimal weight: 5.9990 chunk 403 optimal weight: 20.0000 chunk 332 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 299 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 ** 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** ** M 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 GLN T 26 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 60141 Z= 0.269 Angle : 0.761 14.739 89144 Z= 0.399 Chirality : 0.042 0.334 11180 Planarity : 0.007 0.127 5326 Dihedral : 16.855 178.709 22303 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 25.70 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.97 % Favored : 90.41 % Rotamer Outliers : 0.32 % 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: 0.73 (0.16), residues: 997 sheet: -1.75 (0.23), residues: 419 loop : -2.49 (0.16), residues: 1160 *********************** 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: 7 poor density : 748 time to evaluate : 2.935 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: 7 outliers final: 4 residues processed: 754 average time/residue: 0.5729 time to fit residues: 699.8050 Evaluate side-chains 562 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 558 time to evaluate : 2.885 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4098 time to fit residues: 6.1271 ------------------------------------------------------------------------------- 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: 20.0000 chunk 281 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 178 optimal weight: 8.9990 chunk 251 optimal weight: 20.0000 chunk 375 optimal weight: 1.9990 chunk 397 optimal weight: 30.0000 chunk 196 optimal weight: 7.9990 chunk 355 optimal weight: 0.6980 chunk 107 optimal weight: 20.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 E 56 GLN E 73 ASN G 11 GLN ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN H 78 GLN ** I 23 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 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** T 26 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 60141 Z= 0.253 Angle : 0.722 14.782 89144 Z= 0.377 Chirality : 0.039 0.325 11180 Planarity : 0.006 0.129 5326 Dihedral : 16.555 179.251 22303 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.70 % Favored : 90.80 % Rotamer Outliers : 0.14 % 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: -1.41 (0.16), residues: 2576 helix: 0.84 (0.16), residues: 971 sheet: -1.63 (0.23), residues: 421 loop : -2.24 (0.17), residues: 1184 *********************** 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 716 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 713 time to evaluate : 2.979 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 outliers start: 3 outliers final: 0 residues processed: 714 average time/residue: 0.5661 time to fit residues: 657.7042 Evaluate side-chains 557 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 2.884 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1079 ------------------------------------------------------------------------------- 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: 2.9990 chunk 225 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 295 optimal weight: 20.0000 chunk 163 optimal weight: 7.9990 chunk 339 optimal weight: 10.0000 chunk 274 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 356 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS ** B 140 HIS ** 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 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** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS J 68 HIS ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN J 78 ASN ** 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 9 GLN ** M 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 ASN T 26 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.122 60141 Z= 0.357 Angle : 0.792 14.600 89144 Z= 0.409 Chirality : 0.042 0.424 11180 Planarity : 0.007 0.129 5326 Dihedral : 16.678 179.696 22303 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 31.06 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.20 % Favored : 90.30 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % 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: -1.65 (0.16), residues: 2576 helix: 0.43 (0.16), residues: 970 sheet: -1.65 (0.23), residues: 426 loop : -2.21 (0.17), residues: 1180 *********************** 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 673 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 669 time to evaluate : 3.042 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 outliers start: 4 outliers final: 1 residues processed: 671 average time/residue: 0.5715 time to fit residues: 626.9929 Evaluate side-chains 527 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 526 time to evaluate : 2.891 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5024 time to fit residues: 3.9760 ------------------------------------------------------------------------------- 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: 9.9990 chunk 357 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 397 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN D 103 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN F 94 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN K 26 ASN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN ** M 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 ASN T 26 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.091 60141 Z= 0.348 Angle : 0.789 14.501 89144 Z= 0.406 Chirality : 0.042 0.331 11180 Planarity : 0.007 0.130 5326 Dihedral : 16.744 179.751 22303 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 30.91 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.70 % Favored : 89.87 % Rotamer Outliers : 0.18 % 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: -1.67 (0.16), residues: 2576 helix: 0.23 (0.16), residues: 969 sheet: -1.49 (0.24), residues: 403 loop : -2.11 (0.17), residues: 1204 *********************** 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 664 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 660 time to evaluate : 2.859 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 outliers start: 4 outliers final: 2 residues processed: 664 average time/residue: 0.5585 time to fit residues: 610.0353 Evaluate side-chains 518 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 516 time to evaluate : 2.911 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4607 time to fit residues: 4.7730 ------------------------------------------------------------------------------- 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: 30.0000 chunk 44 optimal weight: 20.0000 chunk 226 optimal weight: 2.9990 chunk 290 optimal weight: 0.4980 chunk 224 optimal weight: 6.9990 chunk 334 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 396 optimal weight: 20.0000 chunk 247 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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** ** 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** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN G 51 GLN H 15 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 HIS T 26 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5705 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= 0.196 Angle : 0.687 14.230 89144 Z= 0.356 Chirality : 0.037 0.398 11180 Planarity : 0.006 0.130 5326 Dihedral : 16.360 179.301 22303 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.80 % Favored : 91.73 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % 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: -1.43 (0.16), residues: 2576 helix: 0.39 (0.16), residues: 967 sheet: -1.37 (0.25), residues: 392 loop : -1.93 (0.17), residues: 1217 *********************** 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 679 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 678 time to evaluate : 3.013 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 outliers start: 1 outliers final: 1 residues processed: 679 average time/residue: 0.5787 time to fit residues: 641.6499 Evaluate side-chains 523 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 522 time to evaluate : 2.897 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4644 time to fit residues: 3.9320 ------------------------------------------------------------------------------- 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: 30.0000 chunk 236 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 195 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 311 optimal weight: 0.8980 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 113 HIS ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 170 GLN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS J 69 ASN J 76 ASN ** 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 60141 Z= 0.189 Angle : 0.677 14.137 89144 Z= 0.351 Chirality : 0.036 0.305 11180 Planarity : 0.006 0.131 5326 Dihedral : 16.187 179.978 22303 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.04 % Favored : 91.50 % Rotamer Outliers : 0.05 % 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: -1.36 (0.16), residues: 2576 helix: 0.44 (0.17), residues: 967 sheet: -1.33 (0.24), residues: 424 loop : -1.87 (0.18), residues: 1185 *********************** 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 675 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 674 time to evaluate : 2.872 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 outliers start: 1 outliers final: 1 residues processed: 675 average time/residue: 0.5644 time to fit residues: 629.1023 Evaluate side-chains 526 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 525 time to evaluate : 2.897 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4281 time to fit residues: 3.8160 ------------------------------------------------------------------------------- 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: 10.0000 chunk 379 optimal weight: 10.0000 chunk 346 optimal weight: 8.9990 chunk 369 optimal weight: 10.0000 chunk 222 optimal weight: 0.8980 chunk 160 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 chunk 333 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 chunk 367 optimal weight: 3.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN B 113 HIS ** 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** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 86 GLN H 70 GLN J 76 ASN ** 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.227 60141 Z= 0.255 Angle : 0.708 16.566 89144 Z= 0.368 Chirality : 0.038 0.401 11180 Planarity : 0.006 0.130 5326 Dihedral : 16.201 179.795 22303 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.39 % Favored : 91.15 % 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: -1.33 (0.16), residues: 2576 helix: 0.36 (0.17), residues: 959 sheet: -1.15 (0.25), residues: 400 loop : -1.81 (0.17), residues: 1217 *********************** 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 649 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 649 time to evaluate : 3.470 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 outliers start: 0 outliers final: 0 residues processed: 649 average time/residue: 0.5520 time to fit residues: 594.4138 Evaluate side-chains 527 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 527 time to evaluate : 2.849 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0981 ------------------------------------------------------------------------------- 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: 9.9990 chunk 390 optimal weight: 0.8980 chunk 238 optimal weight: 30.0000 chunk 185 optimal weight: 0.0870 chunk 271 optimal weight: 0.0570 chunk 409 optimal weight: 30.0000 chunk 376 optimal weight: 8.9990 chunk 326 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 overall best weight: 3.4080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN J 76 ASN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN ** M 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 HIS T 26 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.6114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.557 60141 Z= 0.253 Angle : 0.756 69.523 89144 Z= 0.382 Chirality : 0.037 0.329 11180 Planarity : 0.007 0.163 5326 Dihedral : 16.166 179.703 22303 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 25.23 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.42 % Favored : 91.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.39 (0.16), residues: 2576 helix: 0.22 (0.16), residues: 969 sheet: -1.17 (0.25), residues: 404 loop : -1.77 (0.18), residues: 1203 ********************** 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 647 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 647 time to evaluate : 2.846 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 outliers start: 0 outliers final: 0 residues processed: 647 average time/residue: 0.5572 time to fit residues: 601.0919 Evaluate side-chains 519 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 2.866 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0929 ------------------------------------------------------------------------------- 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: 5.9990 chunk 347 optimal weight: 3.9990 chunk 99 optimal weight: 30.0000 chunk 300 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 326 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 335 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- 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 C 3 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN G 68 ASN G 84 ASN G 97 GLN J 76 ASN ** 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 14 HIS T 26 ASN W 43 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.065424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.054514 restraints weight = 294805.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.056074 restraints weight = 118735.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.056924 restraints weight = 65010.136| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.6280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.378 60141 Z= 0.341 Angle : 0.795 34.416 89144 Z= 0.410 Chirality : 0.040 0.366 11180 Planarity : 0.008 0.143 5326 Dihedral : 16.405 179.880 22303 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 30.98 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.51 % Favored : 90.02 % Rotamer Outliers : 0.05 % 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: -1.66 (0.16), residues: 2576 helix: -0.12 (0.16), residues: 976 sheet: -1.17 (0.25), residues: 407 loop : -1.90 (0.18), residues: 1193 =============================================================================== Job complete usr+sys time: 10517.67 seconds wall clock time: 187 minutes 50.37 seconds (11270.37 seconds total)