Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 17:39:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/04_2023/5ll6_4071_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/04_2023/5ll6_4071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/04_2023/5ll6_4071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/04_2023/5ll6_4071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/04_2023/5ll6_4071_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/04_2023/5ll6_4071_updated.pdb" } resolution = 3.9 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 8 7.16 5 P 1331 5.49 5 Mg 1 5.21 5 S 72 5.16 5 C 29720 2.51 5 N 10027 2.21 5 O 14103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 41": "NH1" <-> "NH2" Residue "P PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 87": "NH1" <-> "NH2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 144": "NH1" <-> "NH2" Residue "Q ARG 152": "NH1" <-> "NH2" Residue "Q ARG 213": "NH1" <-> "NH2" Residue "R PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 91": "NH1" <-> "NH2" Residue "R PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "S ARG 11": "NH1" <-> "NH2" Residue "S TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 49": "NH1" <-> "NH2" Residue "S ARG 59": "NH1" <-> "NH2" Residue "S ARG 108": "NH1" <-> "NH2" Residue "S TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 200": "NH1" <-> "NH2" Residue "S ARG 252": "NH1" <-> "NH2" Residue "T ARG 23": "NH1" <-> "NH2" Residue "T TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 92": "NH1" <-> "NH2" Residue "T ARG 98": "NH1" <-> "NH2" Residue "T ARG 137": "NH1" <-> "NH2" Residue "T ARG 191": "NH1" <-> "NH2" Residue "U ARG 39": "NH1" <-> "NH2" Residue "U PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 104": "NH1" <-> "NH2" Residue "U TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 8": "NH1" <-> "NH2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ARG 47": "NH1" <-> "NH2" Residue "V ARG 59": "NH1" <-> "NH2" Residue "V PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 110": "NH1" <-> "NH2" Residue "V ARG 164": "NH1" <-> "NH2" Residue "V ARG 178": "NH1" <-> "NH2" Residue "V ARG 194": "NH1" <-> "NH2" Residue "W ARG 3": "NH1" <-> "NH2" Residue "W TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 17": "NH1" <-> "NH2" Residue "W ARG 53": "NH1" <-> "NH2" Residue "W ARG 54": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 78": "NH1" <-> "NH2" Residue "W ARG 168": "NH1" <-> "NH2" Residue "W ARG 171": "NH1" <-> "NH2" Residue "X ARG 30": "NH1" <-> "NH2" Residue "X ARG 33": "NH1" <-> "NH2" Residue "X TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 116": "NH1" <-> "NH2" Residue "Y ARG 104": "NH1" <-> "NH2" Residue "Y ARG 106": "NH1" <-> "NH2" Residue "Y PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 90": "NH1" <-> "NH2" Residue "Z ARG 103": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "a ARG 60": "NH1" <-> "NH2" Residue "a ARG 71": "NH1" <-> "NH2" Residue "b PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 16": "NH1" <-> "NH2" Residue "c ARG 19": "NH1" <-> "NH2" Residue "c ARG 144": "NH1" <-> "NH2" Residue "d ARG 20": "NH1" <-> "NH2" Residue "d PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 32": "NH1" <-> "NH2" Residue "d PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 10": "NH1" <-> "NH2" Residue "e ARG 51": "NH1" <-> "NH2" Residue "e TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 54": "NH1" <-> "NH2" Residue "h ARG 22": "NH1" <-> "NH2" Residue "h PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 96": "NH1" <-> "NH2" Residue "h ARG 101": "NH1" <-> "NH2" Residue "h GLU 151": "OE1" <-> "OE2" Residue "h TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 162": "OD1" <-> "OD2" Residue "h ARG 194": "NH1" <-> "NH2" Residue "h ASP 218": "OD1" <-> "OD2" Residue "h PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 241": "OD1" <-> "OD2" Residue "h PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 289": "OD1" <-> "OD2" Residue "h ARG 311": "NH1" <-> "NH2" Residue "h ARG 328": "NH1" <-> "NH2" Residue "h PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 487": "OD1" <-> "OD2" Residue "h ASP 492": "OD1" <-> "OD2" Residue "h ASP 499": "OD1" <-> "OD2" Residue "h TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 573": "NH1" <-> "NH2" Residue "h ASP 591": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 55262 Number of models: 1 Model: "" Number of chains: 20 Chain: "2" Number of atoms: 28237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1325, 28237 Classifications: {'RNA': 1325} Modifications used: {'rna2p_pur': 51, 'rna2p_pyr': 42, 'rna3p_pur': 652, 'rna3p_pyr': 580} Link IDs: {'rna2p': 93, 'rna3p': 1231} Chain breaks: 5 Chain: "P" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1577 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 189} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "Q" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1709 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "R" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1717 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "S" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "T" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1799 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 216} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "U" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1481 Classifications: {'peptide': 184} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 172} Chain: "V" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "W" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "X" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1213 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 146} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "Y" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 142} Chain: "Z" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 891 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "a" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 684 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "b" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "c" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} Chain: "d" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1060 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "e" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 769 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "f" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "g" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 473 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 54} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4657 Unusual residues: {' MG': 1, 'ANP': 2, 'SF4': 2} Classifications: {'peptide': 578, 'undetermined': 5} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 543, None: 5} Not linked: pdbres="ASP h 604 " pdbres="SF4 h 701 " Not linked: pdbres="SF4 h 701 " pdbres="SF4 h 702 " Not linked: pdbres="SF4 h 702 " pdbres="ANP h 703 " Not linked: pdbres="ANP h 703 " pdbres=" MG h 704 " Not linked: pdbres=" MG h 704 " pdbres="ANP h 705 " Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 50808 SG CYS h 29 93.313 94.937 142.717 1.00 35.87 S ATOM 51001 SG CYS h 55 99.342 94.944 146.873 1.00 50.48 S ATOM 51037 SG CYS h 61 97.871 98.555 141.785 1.00 25.67 S ATOM 51019 SG CYS h 58 99.197 93.384 141.760 1.00 31.14 S ATOM 50776 SG CYS h 25 94.684 103.092 141.529 1.00 38.66 S ATOM 50741 SG CYS h 21 90.903 108.408 139.545 1.00 48.90 S ATOM 51068 SG CYS h 65 96.483 105.973 139.307 1.00 47.82 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A 21756 " occ=0.55 ... (20 atoms not shown) pdb=" C4 A 21756 " occ=0.55 Time building chain proxies: 21.06, per 1000 atoms: 0.38 Number of scatterers: 55262 At special positions: 0 Unit cell: (210.296, 185.364, 220.052, 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) Fe 8 26.01 S 72 16.00 P 1331 15.00 Mg 1 11.99 O 14103 8.00 N 10027 7.00 C 29720 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: 20.20 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 h 701 " pdb="FE4 SF4 h 701 " - pdb=" SG CYS h 58 " pdb="FE3 SF4 h 701 " - pdb=" SG CYS h 61 " pdb="FE2 SF4 h 701 " - pdb=" SG CYS h 55 " pdb="FE1 SF4 h 701 " - pdb=" SG CYS h 29 " pdb=" SF4 h 702 " pdb="FE2 SF4 h 702 " - pdb=" SG CYS h 21 " pdb="FE3 SF4 h 702 " - pdb=" SG CYS h 65 " pdb="FE1 SF4 h 702 " - pdb=" SG CYS h 25 " pdb="FE4 SF4 h 702 " - pdb=" SG CYS h 16 " Number of angles added : 24 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 36 sheets defined 27.8% alpha, 10.8% beta 347 base pairs and 637 stacking pairs defined. Time for finding SS restraints: 16.52 Creating SS restraints... Processing helix chain 'P' and resid 11 through 20 Processing helix chain 'P' and resid 50 through 66 Processing helix chain 'P' and resid 80 through 92 Processing helix chain 'P' and resid 130 through 138 removed outlier: 3.537A pdb=" N SER P 137 " --> pdb=" O ILE P 133 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR P 138 " --> pdb=" O LYS P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 170 through 183 Processing helix chain 'Q' and resid 58 through 61 No H-bonds generated for 'chain 'Q' and resid 58 through 61' Processing helix chain 'Q' and resid 70 through 74 Processing helix chain 'Q' and resid 107 through 113 Processing helix chain 'Q' and resid 159 through 175 Processing helix chain 'Q' and resid 180 through 190 removed outlier: 3.750A pdb=" N LEU Q 184 " --> pdb=" O THR Q 180 " (cutoff:3.500A) Proline residue: Q 190 - end of helix Processing helix chain 'Q' and resid 193 through 203 removed outlier: 4.173A pdb=" N ASP Q 203 " --> pdb=" O ASN Q 199 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 230 Processing helix chain 'R' and resid 39 through 47 removed outlier: 4.469A pdb=" N ARG R 43 " --> pdb=" O THR R 39 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU R 44 " --> pdb=" O LYS R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 59 Processing helix chain 'R' and resid 67 through 72 removed outlier: 3.621A pdb=" N THR R 71 " --> pdb=" O GLN R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 134 Processing helix chain 'R' and resid 182 through 191 Processing helix chain 'R' and resid 207 through 221 removed outlier: 4.218A pdb=" N LYS R 212 " --> pdb=" O GLU R 208 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR R 221 " --> pdb=" O ALA R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 229 No H-bonds generated for 'chain 'R' and resid 227 through 229' Processing helix chain 'R' and resid 239 through 242 No H-bonds generated for 'chain 'R' and resid 239 through 242' Processing helix chain 'S' and resid 16 through 18 No H-bonds generated for 'chain 'S' and resid 16 through 18' Processing helix chain 'S' and resid 44 through 49 Processing helix chain 'S' and resid 58 through 65 Processing helix chain 'S' and resid 72 through 74 No H-bonds generated for 'chain 'S' and resid 72 through 74' Processing helix chain 'S' and resid 94 through 96 No H-bonds generated for 'chain 'S' and resid 94 through 96' Processing helix chain 'S' and resid 118 through 120 No H-bonds generated for 'chain 'S' and resid 118 through 120' Processing helix chain 'S' and resid 133 through 135 No H-bonds generated for 'chain 'S' and resid 133 through 135' Processing helix chain 'S' and resid 248 through 254 Processing helix chain 'T' and resid 22 through 24 No H-bonds generated for 'chain 'T' and resid 22 through 24' Processing helix chain 'T' and resid 58 through 60 No H-bonds generated for 'chain 'T' and resid 58 through 60' Processing helix chain 'T' and resid 138 through 145 Processing helix chain 'T' and resid 181 through 224 removed outlier: 3.699A pdb=" N GLU T 207 " --> pdb=" O GLU T 203 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR T 208 " --> pdb=" O ALA T 204 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU T 222 " --> pdb=" O GLU T 218 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS T 223 " --> pdb=" O ARG T 219 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA T 224 " --> pdb=" O LYS T 220 " (cutoff:3.500A) Processing helix chain 'U' and resid 6 through 9 No H-bonds generated for 'chain 'U' and resid 6 through 9' Processing helix chain 'U' and resid 15 through 28 Processing helix chain 'U' and resid 67 through 73 removed outlier: 3.723A pdb=" N LYS U 72 " --> pdb=" O ALA U 68 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL U 73 " --> pdb=" O GLY U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 83 removed outlier: 3.512A pdb=" N LYS U 83 " --> pdb=" O ARG U 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 116 No H-bonds generated for 'chain 'U' and resid 114 through 116' Processing helix chain 'U' and resid 118 through 129 Processing helix chain 'U' and resid 167 through 176 removed outlier: 3.628A pdb=" N GLN U 170 " --> pdb=" O GLU U 167 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA U 171 " --> pdb=" O SER U 168 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU U 176 " --> pdb=" O TYR U 173 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 93 No H-bonds generated for 'chain 'V' and resid 90 through 93' Processing helix chain 'V' and resid 107 through 116 Processing helix chain 'V' and resid 137 through 145 Processing helix chain 'V' and resid 154 through 162 Processing helix chain 'V' and resid 173 through 176 No H-bonds generated for 'chain 'V' and resid 173 through 176' Processing helix chain 'V' and resid 186 through 196 Processing helix chain 'W' and resid 21 through 34 removed outlier: 3.513A pdb=" N ASP W 25 " --> pdb=" O SER W 21 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS W 29 " --> pdb=" O ASP W 25 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 60 Processing helix chain 'W' and resid 67 through 83 removed outlier: 3.554A pdb=" N PHE W 71 " --> pdb=" O PRO W 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 98 No H-bonds generated for 'chain 'W' and resid 95 through 98' Processing helix chain 'W' and resid 101 through 107 Processing helix chain 'W' and resid 109 through 116 removed outlier: 3.656A pdb=" N VAL W 113 " --> pdb=" O LEU W 109 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR W 114 " --> pdb=" O GLN W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 122 through 130 Processing helix chain 'W' and resid 153 through 155 No H-bonds generated for 'chain 'W' and resid 153 through 155' Processing helix chain 'W' and resid 172 through 177 Processing helix chain 'X' and resid 46 through 49 No H-bonds generated for 'chain 'X' and resid 46 through 49' Processing helix chain 'Y' and resid 31 through 43 Processing helix chain 'Y' and resid 47 through 56 Processing helix chain 'Y' and resid 63 through 66 No H-bonds generated for 'chain 'Y' and resid 63 through 66' Processing helix chain 'Y' and resid 71 through 78 Processing helix chain 'Y' and resid 86 through 104 Processing helix chain 'Y' and resid 110 through 131 removed outlier: 3.534A pdb=" N ARG Y 127 " --> pdb=" O HIS Y 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR Y 128 " --> pdb=" O ARG Y 124 " (cutoff:3.500A) Processing helix chain 'Y' and resid 146 through 150 Processing helix chain 'Z' and resid 44 through 46 No H-bonds generated for 'chain 'Z' and resid 44 through 46' Processing helix chain 'Z' and resid 52 through 55 removed outlier: 4.001A pdb=" N SER Z 55 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 52 through 55' Processing helix chain 'Z' and resid 57 through 74 removed outlier: 3.573A pdb=" N LEU Z 62 " --> pdb=" O TYR Z 58 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN Z 65 " --> pdb=" O MET Z 61 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA Z 69 " --> pdb=" O GLN Z 65 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS Z 70 " --> pdb=" O ASP Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 96 through 106 removed outlier: 4.257A pdb=" N ALA Z 100 " --> pdb=" O PRO Z 96 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 62 Processing helix chain 'a' and resid 65 through 76 removed outlier: 3.545A pdb=" N ASP a 76 " --> pdb=" O LEU a 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 6 through 20 Processing helix chain 'b' and resid 32 through 44 removed outlier: 3.739A pdb=" N HIS b 44 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 93 Processing helix chain 'b' and resid 113 through 119 Processing helix chain 'c' and resid 12 through 22 Processing helix chain 'c' and resid 27 through 33 Processing helix chain 'c' and resid 36 through 39 No H-bonds generated for 'chain 'c' and resid 36 through 39' Processing helix chain 'c' and resid 132 through 136 Processing helix chain 'd' and resid 37 through 46 removed outlier: 4.256A pdb=" N ALA d 45 " --> pdb=" O ARG d 41 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU d 46 " --> pdb=" O GLU d 42 " (cutoff:3.500A) Processing helix chain 'd' and resid 79 through 85 Processing helix chain 'd' and resid 88 through 94 removed outlier: 3.728A pdb=" N VAL d 92 " --> pdb=" O THR d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 117 Processing helix chain 'd' and resid 123 through 132 Processing helix chain 'e' and resid 50 through 55 Processing helix chain 'e' and resid 76 through 80 Processing helix chain 'f' and resid 12 through 17 removed outlier: 3.651A pdb=" N ARG f 17 " --> pdb=" O ALA f 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 13 through 17 Processing helix chain 'g' and resid 33 through 43 Processing helix chain 'h' and resid 18 through 21 No H-bonds generated for 'chain 'h' and resid 18 through 21' Processing helix chain 'h' and resid 24 through 27 No H-bonds generated for 'chain 'h' and resid 24 through 27' Processing helix chain 'h' and resid 32 through 34 No H-bonds generated for 'chain 'h' and resid 32 through 34' Processing helix chain 'h' and resid 60 through 63 No H-bonds generated for 'chain 'h' and resid 60 through 63' Processing helix chain 'h' and resid 116 through 124 Processing helix chain 'h' and resid 140 through 146 Processing helix chain 'h' and resid 151 through 161 removed outlier: 3.629A pdb=" N PHE h 156 " --> pdb=" O GLN h 153 " (cutoff:3.500A) Processing helix chain 'h' and resid 174 through 179 removed outlier: 4.024A pdb=" N ARG h 178 " --> pdb=" O ASP h 174 " (cutoff:3.500A) Processing helix chain 'h' and resid 188 through 194 removed outlier: 3.634A pdb=" N LYS h 192 " --> pdb=" O GLY h 188 " (cutoff:3.500A) Processing helix chain 'h' and resid 200 through 208 Processing helix chain 'h' and resid 224 through 237 Processing helix chain 'h' and resid 254 through 267 removed outlier: 3.924A pdb=" N LEU h 258 " --> pdb=" O VAL h 254 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN h 259 " --> pdb=" O LYS h 255 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU h 267 " --> pdb=" O ILE h 263 " (cutoff:3.500A) Processing helix chain 'h' and resid 284 through 287 No H-bonds generated for 'chain 'h' and resid 284 through 287' Processing helix chain 'h' and resid 310 through 319 removed outlier: 3.749A pdb=" N ASP h 319 " --> pdb=" O ASN h 315 " (cutoff:3.500A) Processing helix chain 'h' and resid 391 through 399 removed outlier: 3.833A pdb=" N ILE h 395 " --> pdb=" O LYS h 391 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 436 removed outlier: 4.002A pdb=" N LYS h 436 " --> pdb=" O GLN h 432 " (cutoff:3.500A) Processing helix chain 'h' and resid 447 through 450 No H-bonds generated for 'chain 'h' and resid 447 through 450' Processing helix chain 'h' and resid 458 through 461 No H-bonds generated for 'chain 'h' and resid 458 through 461' Processing helix chain 'h' and resid 470 through 479 Processing helix chain 'h' and resid 500 through 516 removed outlier: 3.746A pdb=" N ILE h 504 " --> pdb=" O SER h 500 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE h 505 " --> pdb=" O GLU h 501 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS h 506 " --> pdb=" O GLN h 502 " (cutoff:3.500A) Processing helix chain 'h' and resid 528 through 532 Processing helix chain 'h' and resid 557 through 568 removed outlier: 3.768A pdb=" N ASN h 567 " --> pdb=" O ARG h 563 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU h 568 " --> pdb=" O PHE h 564 " (cutoff:3.500A) Processing helix chain 'h' and resid 589 through 597 removed outlier: 3.526A pdb=" N GLU h 593 " --> pdb=" O GLN h 589 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'P' and resid 74 through 76 removed outlier: 7.785A pdb=" N VAL P 123 " --> pdb=" O PRO P 142 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE P 144 " --> pdb=" O VAL P 123 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'P' and resid 37 through 41 removed outlier: 3.540A pdb=" N VAL P 47 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA P 40 " --> pdb=" O VAL P 45 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL P 45 " --> pdb=" O ALA P 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'Q' and resid 65 through 69 Processing sheet with id= D, first strand: chain 'Q' and resid 124 through 128 Processing sheet with id= E, first strand: chain 'Q' and resid 29 through 33 Processing sheet with id= F, first strand: chain 'R' and resid 81 through 89 removed outlier: 4.014A pdb=" N HIS R 110 " --> pdb=" O ASP R 106 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 158 through 162 Processing sheet with id= H, first strand: chain 'S' and resid 89 through 91 Processing sheet with id= I, first strand: chain 'S' and resid 122 through 125 removed outlier: 3.593A pdb=" N THR S 159 " --> pdb=" O ILE S 173 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP S 171 " --> pdb=" O LYS S 161 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 128 through 131 removed outlier: 3.872A pdb=" N LYS S 128 " --> pdb=" O VAL S 140 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 207 through 211 Processing sheet with id= L, first strand: chain 'T' and resid 12 through 17 removed outlier: 3.689A pdb=" N LEU T 109 " --> pdb=" O LYS T 2 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY T 54 " --> pdb=" O ALA T 110 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'T' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'T' and resid 72 through 77 Processing sheet with id= O, first strand: chain 'U' and resid 46 through 50 Processing sheet with id= P, first strand: chain 'U' and resid 180 through 185 removed outlier: 3.949A pdb=" N GLN U 180 " --> pdb=" O LYS U 148 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V' and resid 42 through 46 Processing sheet with id= R, first strand: chain 'V' and resid 62 through 66 Processing sheet with id= S, first strand: chain 'V' and resid 181 through 183 removed outlier: 3.908A pdb=" N ALA V 100 " --> pdb=" O ILE V 169 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'X' and resid 99 through 110 removed outlier: 3.627A pdb=" N ARG X 99 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA X 89 " --> pdb=" O THR X 72 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR X 72 " --> pdb=" O ALA X 89 " (cutoff:3.500A) removed outlier: 14.161A pdb=" N LEU X 91 " --> pdb=" O ILE X 70 " (cutoff:3.500A) removed outlier: 16.766A pdb=" N ILE X 70 " --> pdb=" O LEU X 91 " (cutoff:3.500A) removed outlier: 22.639A pdb=" N TYR X 93 " --> pdb=" O GLY X 68 " (cutoff:3.500A) removed outlier: 26.250A pdb=" N GLY X 68 " --> pdb=" O TYR X 93 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS X 69 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL X 125 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU X 71 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL X 123 " --> pdb=" O LEU X 71 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY X 126 " --> pdb=" O VAL X 139 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL X 139 " --> pdb=" O GLY X 126 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'Z' and resid 80 through 83 removed outlier: 5.828A pdb=" N ARG Z 114 " --> pdb=" O VAL Z 81 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE Z 83 " --> pdb=" O ARG Z 114 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU Z 116 " --> pdb=" O ILE Z 83 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'a' and resid 32 through 37 Processing sheet with id= W, first strand: chain 'b' and resid 24 through 27 Processing sheet with id= X, first strand: chain 'b' and resid 71 through 73 Processing sheet with id= Y, first strand: chain 'c' and resid 54 through 56 Processing sheet with id= Z, first strand: chain 'd' and resid 13 through 15 Processing sheet with id= AA, first strand: chain 'd' and resid 60 through 62 Processing sheet with id= AB, first strand: chain 'd' and resid 5 through 10 removed outlier: 4.648A pdb=" N ILE d 7 " --> pdb=" O ASP d 26 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP d 26 " --> pdb=" O ILE d 7 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR d 9 " --> pdb=" O VAL d 24 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL d 24 " --> pdb=" O THR d 9 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'e' and resid 20 through 22 Processing sheet with id= AD, first strand: chain 'e' and resid 38 through 43 Processing sheet with id= AE, first strand: chain 'f' and resid 32 through 35 Processing sheet with id= AF, first strand: chain 'h' and resid 6 through 10 removed outlier: 3.761A pdb=" N SER h 6 " --> pdb=" O LEU h 75 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'h' and resid 242 through 246 removed outlier: 6.380A pdb=" N TYR h 273 " --> pdb=" O TYR h 243 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N PHE h 245 " --> pdb=" O TYR h 273 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE h 275 " --> pdb=" O PHE h 245 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'h' and resid 294 through 297 Processing sheet with id= AI, first strand: chain 'h' and resid 360 through 362 removed outlier: 3.722A pdb=" N ALA h 551 " --> pdb=" O ASN h 369 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL h 540 " --> pdb=" O ARG h 552 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ILE h 539 " --> pdb=" O ILE h 380 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL h 382 " --> pdb=" O ILE h 539 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE h 541 " --> pdb=" O VAL h 382 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N MET h 384 " --> pdb=" O PHE h 541 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA h 521 " --> pdb=" O GLU h 379 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'h' and resid 572 through 574 683 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 842 hydrogen bonds 1434 hydrogen bond angles 0 basepair planarities 347 basepair parallelities 637 stacking parallelities Total time for adding SS restraints: 26.56 Time building geometry restraints manager: 22.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.36: 15282 1.36 - 1.65: 43685 1.65 - 1.94: 99 1.94 - 2.23: 24 2.23 - 2.52: 2 Bond restraints: 59092 Sorted by residual: bond pdb=" CG ASP h 14 " pdb=" OD1 ASP h 14 " ideal model delta sigma weight residual 1.249 2.520 -1.271 1.90e-02 2.77e+03 4.48e+03 bond pdb=" CG ASP h 14 " pdb=" OD2 ASP h 14 " ideal model delta sigma weight residual 1.249 2.401 -1.152 1.90e-02 2.77e+03 3.68e+03 bond pdb=" O3' U 21761 " pdb=" P A 21762 " ideal model delta sigma weight residual 1.607 1.070 0.537 1.50e-02 4.44e+03 1.28e+03 bond pdb=" O3' C 21636 " pdb=" P C 21637 " ideal model delta sigma weight residual 1.607 1.241 0.366 1.50e-02 4.44e+03 5.96e+02 bond pdb=" CA ARG h 101 " pdb=" C ARG h 101 " ideal model delta sigma weight residual 1.524 1.724 -0.200 1.26e-02 6.30e+03 2.53e+02 ... (remaining 59087 not shown) Histogram of bond angle deviations from ideal: 33.91 - 54.66: 3 54.66 - 75.42: 1 75.42 - 96.18: 47 96.18 - 116.93: 51002 116.93 - 137.69: 35211 Bond angle restraints: 86264 Sorted by residual: angle pdb=" CB ASP h 14 " pdb=" CG ASP h 14 " pdb=" OD2 ASP h 14 " ideal model delta sigma weight residual 118.40 33.91 84.49 2.30e+00 1.89e-01 1.35e+03 angle pdb=" OD1 ASP h 14 " pdb=" CG ASP h 14 " pdb=" OD2 ASP h 14 " ideal model delta sigma weight residual 122.90 52.95 69.95 2.40e+00 1.74e-01 8.49e+02 angle pdb=" CB ASP h 14 " pdb=" CG ASP h 14 " pdb=" OD1 ASP h 14 " ideal model delta sigma weight residual 118.40 51.77 66.63 2.30e+00 1.89e-01 8.39e+02 angle pdb=" CA THR h 99 " pdb=" C THR h 99 " pdb=" N PRO h 100 " ideal model delta sigma weight residual 118.44 74.68 43.76 1.59e+00 3.96e-01 7.57e+02 angle pdb="FE2 SF4 h 701 " pdb=" S4 SF4 h 701 " pdb="FE3 SF4 h 701 " ideal model delta sigma weight residual 73.70 100.56 -26.86 1.50e+00 4.44e-01 3.21e+02 ... (remaining 86259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 31067 35.83 - 71.66: 1528 71.66 - 107.49: 180 107.49 - 143.32: 28 143.32 - 179.15: 34 Dihedral angle restraints: 32837 sinusoidal: 22954 harmonic: 9883 Sorted by residual: dihedral pdb=" C5' U 2 128 " pdb=" C4' U 2 128 " pdb=" C3' U 2 128 " pdb=" O3' U 2 128 " ideal model delta sinusoidal sigma weight residual 147.00 73.35 73.65 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" C5' U 2 159 " pdb=" C4' U 2 159 " pdb=" C3' U 2 159 " pdb=" O3' U 2 159 " ideal model delta sinusoidal sigma weight residual 147.00 73.81 73.19 1 8.00e+00 1.56e-02 1.07e+02 dihedral pdb=" C5' U 2 721 " pdb=" C4' U 2 721 " pdb=" C3' U 2 721 " pdb=" O3' U 2 721 " ideal model delta sinusoidal sigma weight residual 147.00 74.39 72.61 1 8.00e+00 1.56e-02 1.05e+02 ... (remaining 32834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.222: 10402 0.222 - 0.443: 362 0.443 - 0.665: 20 0.665 - 0.887: 9 0.887 - 1.109: 3 Chirality restraints: 10796 Sorted by residual: chirality pdb="FE3 SF4 h 701 " pdb=" S1 SF4 h 701 " pdb=" S2 SF4 h 701 " pdb=" S4 SF4 h 701 " both_signs ideal model delta sigma weight residual False -10.55 -9.45 -1.11 2.00e-01 2.50e+01 3.07e+01 chirality pdb="FE2 SF4 h 701 " pdb=" S1 SF4 h 701 " pdb=" S3 SF4 h 701 " pdb=" S4 SF4 h 701 " both_signs ideal model delta sigma weight residual False 10.55 9.59 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb="FE2 SF4 h 702 " pdb=" S1 SF4 h 702 " pdb=" S3 SF4 h 702 " pdb=" S4 SF4 h 702 " both_signs ideal model delta sigma weight residual False 10.55 9.66 0.89 2.00e-01 2.50e+01 2.00e+01 ... (remaining 10793 not shown) Planarity restraints: 6060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP h 14 " -0.572 2.00e-02 2.50e+03 3.43e-01 1.18e+03 pdb=" CG ASP h 14 " 0.255 2.00e-02 2.50e+03 pdb=" OD1 ASP h 14 " 0.037 2.00e-02 2.50e+03 pdb=" OD2 ASP h 14 " 0.279 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR h 99 " -0.014 2.00e-02 2.50e+03 1.94e-01 3.76e+02 pdb=" C THR h 99 " 0.319 2.00e-02 2.50e+03 pdb=" O THR h 99 " -0.180 2.00e-02 2.50e+03 pdb=" N PRO h 100 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 8 " 0.042 2.00e-02 2.50e+03 9.24e-02 1.92e+02 pdb=" N1 U 2 8 " -0.035 2.00e-02 2.50e+03 pdb=" C2 U 2 8 " -0.017 2.00e-02 2.50e+03 pdb=" O2 U 2 8 " -0.114 2.00e-02 2.50e+03 pdb=" N3 U 2 8 " 0.215 2.00e-02 2.50e+03 pdb=" C4 U 2 8 " 0.042 2.00e-02 2.50e+03 pdb=" O4 U 2 8 " -0.109 2.00e-02 2.50e+03 pdb=" C5 U 2 8 " -0.026 2.00e-02 2.50e+03 pdb=" C6 U 2 8 " 0.002 2.00e-02 2.50e+03 ... (remaining 6057 not shown) Histogram of nonbonded interaction distances: 0.92 - 1.72: 19 1.72 - 2.51: 197 2.51 - 3.31: 59522 3.31 - 4.10: 158377 4.10 - 4.90: 245614 Warning: very small nonbonded interaction distances. Nonbonded interactions: 463729 Sorted by model distance: nonbonded pdb=" N1 A 21116 " pdb=" C4 A 21131 " model vdw 0.924 3.340 nonbonded pdb=" C2 A 21116 " pdb=" N1 A 21131 " model vdw 1.191 3.420 nonbonded pdb=" N1 A 21116 " pdb=" C5 A 21131 " model vdw 1.191 3.340 nonbonded pdb=" CA ARG h 148 " pdb=" NE2 GLN h 153 " model vdw 1.194 3.550 nonbonded pdb=" OP1 C 21674 " pdb=" NH1 ARG T 92 " model vdw 1.211 2.520 ... (remaining 463724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.120 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: 0.040 Extract box with map and model: 14.800 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 133.430 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.012 1.271 59092 Z= 0.639 Angle : 1.502 84.493 86264 Z= 0.945 Chirality : 0.108 1.109 10796 Planarity : 0.010 0.343 6060 Dihedral : 19.043 179.146 26453 Min Nonbonded Distance : 0.924 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 3.66 % Allowed : 10.63 % Favored : 85.71 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 0.62 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.12), residues: 3387 helix: -0.98 (0.15), residues: 956 sheet: -3.34 (0.17), residues: 545 loop : -3.30 (0.12), residues: 1886 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1174 time to evaluate : 3.900 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: 73 outliers final: 14 residues processed: 1220 average time/residue: 0.6426 time to fit residues: 1257.0330 Evaluate side-chains 726 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 712 time to evaluate : 3.038 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.4919 time to fit residues: 15.9156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 6.9990 chunk 353 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 chunk 238 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 366 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 424 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 46 HIS P 69 ASN P 140 ASN R 29 ASN ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 ASN S 69 HIS S 98 ASN S 142 HIS S 153 ASN T 22 HIS ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN V 103 GLN V 116 HIS V 119 GLN W 110 GLN W 176 ASN X 8 GLN X 118 GLN a 7 GLN a 81 ASN ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 27 ASN c 99 ASN d 22 GLN d 106 GLN d 107 GLN d 110 GLN e 11 ASN e 80 HIS f 42 ASN h 5 ASN ** h 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 154 ASN h 363 GLN h 446 GLN h 562 ASN h 584 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 59092 Z= 0.196 Angle : 0.737 12.919 86264 Z= 0.377 Chirality : 0.042 0.318 10796 Planarity : 0.006 0.077 6060 Dihedral : 18.198 179.539 19667 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 1.21 % Allowed : 9.65 % Favored : 89.13 % Rotamer Outliers : 5.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 1.25 % Twisted General : 0.12 % 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: -2.77 (0.13), residues: 3387 helix: 0.44 (0.17), residues: 967 sheet: -2.44 (0.18), residues: 581 loop : -3.04 (0.13), residues: 1839 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 833 time to evaluate : 3.007 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: 148 outliers final: 73 residues processed: 917 average time/residue: 0.5726 time to fit residues: 863.2699 Evaluate side-chains 747 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 674 time to evaluate : 3.050 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.4338 time to fit residues: 61.4742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 235 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 424 optimal weight: 3.9990 chunk 458 optimal weight: 0.0570 chunk 378 optimal weight: 9.9990 chunk 421 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 340 optimal weight: 2.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 23 HIS P 83 GLN P 92 HIS Q 101 HIS ** Q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN R 94 GLN S 16 HIS S 130 GLN T 4 ASN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 182 GLN U 11 GLN V 94 ASN V 116 HIS V 159 GLN W 131 GLN W 133 HIS ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 106 ASN Y 101 HIS a 21 ASN a 29 HIS a 81 ASN ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 GLN b 80 ASN ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 63 GLN e 72 HIS f 26 GLN g 17 GLN h 82 HIS h 228 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 59092 Z= 0.331 Angle : 0.781 13.534 86264 Z= 0.397 Chirality : 0.043 0.461 10796 Planarity : 0.006 0.099 6060 Dihedral : 18.190 179.050 19667 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 1.06 % Allowed : 11.16 % Favored : 87.78 % Rotamer Outliers : 5.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 0.62 % Twisted General : 0.03 % 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: -2.74 (0.13), residues: 3387 helix: 0.19 (0.16), residues: 958 sheet: -2.26 (0.19), residues: 598 loop : -2.89 (0.13), residues: 1831 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 733 time to evaluate : 3.137 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 outliers start: 149 outliers final: 75 residues processed: 821 average time/residue: 0.5906 time to fit residues: 814.4830 Evaluate side-chains 710 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 635 time to evaluate : 3.061 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.4056 time to fit residues: 61.8026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 419 optimal weight: 10.0000 chunk 319 optimal weight: 0.9980 chunk 220 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 285 optimal weight: 4.9990 chunk 426 optimal weight: 0.0370 chunk 451 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 404 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 92 HIS P 168 HIS Q 49 ASN Q 101 HIS Q 118 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 176 GLN ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 116 HIS W 131 GLN b 15 ASN c 99 ASN d 63 GLN d 110 GLN g 17 GLN ** h 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 59092 Z= 0.236 Angle : 0.687 14.167 86264 Z= 0.348 Chirality : 0.039 0.290 10796 Planarity : 0.005 0.066 6060 Dihedral : 17.867 179.118 19667 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.83 % Favored : 89.16 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 1.25 % Twisted General : 0.03 % 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: -2.49 (0.14), residues: 3387 helix: 0.38 (0.17), residues: 969 sheet: -2.09 (0.20), residues: 597 loop : -2.75 (0.13), residues: 1821 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 706 time to evaluate : 3.082 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 outliers start: 101 outliers final: 53 residues processed: 765 average time/residue: 0.5717 time to fit residues: 722.5280 Evaluate side-chains 672 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 619 time to evaluate : 3.091 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.4264 time to fit residues: 45.5656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 375 optimal weight: 7.9990 chunk 256 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 336 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 385 optimal weight: 2.9990 chunk 312 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 405 optimal weight: 0.0170 chunk 113 optimal weight: 10.0000 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS R 209 ASN S 209 HIS ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 HIS ** V 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 79 ASN d 110 GLN f 42 ASN ** f 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 59092 Z= 0.320 Angle : 0.763 14.148 86264 Z= 0.385 Chirality : 0.042 0.267 10796 Planarity : 0.006 0.099 6060 Dihedral : 18.024 179.374 19667 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 1.03 % Allowed : 11.28 % Favored : 87.69 % Rotamer Outliers : 4.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 0.62 % Twisted General : 0.03 % 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: -2.59 (0.14), residues: 3387 helix: 0.17 (0.16), residues: 962 sheet: -2.07 (0.20), residues: 593 loop : -2.76 (0.13), residues: 1832 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 660 time to evaluate : 3.136 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 outliers start: 116 outliers final: 68 residues processed: 724 average time/residue: 0.5577 time to fit residues: 678.5159 Evaluate side-chains 665 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 597 time to evaluate : 3.061 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.3975 time to fit residues: 55.2507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 151 optimal weight: 0.7980 chunk 406 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 451 optimal weight: 7.9990 chunk 375 optimal weight: 5.9990 chunk 209 optimal weight: 0.0570 chunk 37 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 237 optimal weight: 0.0970 overall best weight: 0.9298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 101 HIS R 209 ASN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 131 GLN ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 101 HIS d 106 GLN f 49 HIS ** f 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 85 HIS ** h 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 154 ASN h 213 ASN h 315 ASN ** h 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 59092 Z= 0.159 Angle : 0.651 14.130 86264 Z= 0.327 Chirality : 0.037 0.286 10796 Planarity : 0.005 0.066 6060 Dihedral : 17.602 177.990 19667 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 1.03 % Allowed : 9.01 % Favored : 89.96 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 1.25 % Twisted General : 0.03 % 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: -2.26 (0.14), residues: 3387 helix: 0.47 (0.17), residues: 956 sheet: -1.87 (0.21), residues: 552 loop : -2.56 (0.13), residues: 1879 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 705 time to evaluate : 3.130 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 outliers start: 62 outliers final: 26 residues processed: 738 average time/residue: 0.5661 time to fit residues: 699.4374 Evaluate side-chains 648 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 622 time to evaluate : 3.072 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.5027 time to fit residues: 26.6888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 435 optimal weight: 0.0970 chunk 50 optimal weight: 20.0000 chunk 257 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 chunk 380 optimal weight: 10.0000 chunk 252 optimal weight: 0.9980 chunk 450 optimal weight: 9.9990 chunk 281 optimal weight: 4.9990 chunk 274 optimal weight: 0.3980 chunk 207 optimal weight: 4.9990 overall best weight: 2.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS Q 118 GLN R 110 HIS R 209 ASN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 ASN f 42 ASN h 5 ASN ** h 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 59092 Z= 0.200 Angle : 0.661 14.092 86264 Z= 0.332 Chirality : 0.037 0.246 10796 Planarity : 0.005 0.067 6060 Dihedral : 17.535 177.969 19667 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 1.00 % Allowed : 10.48 % Favored : 88.51 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 0.62 % Twisted General : 0.03 % 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: -2.24 (0.14), residues: 3387 helix: 0.46 (0.17), residues: 957 sheet: -1.89 (0.21), residues: 545 loop : -2.52 (0.13), residues: 1885 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 654 time to evaluate : 3.111 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 outliers start: 70 outliers final: 43 residues processed: 689 average time/residue: 0.5597 time to fit residues: 650.1556 Evaluate side-chains 657 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 614 time to evaluate : 3.064 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3949 time to fit residues: 36.0623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 278 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 268 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 306 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 353 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 29 HIS e 80 HIS h 5 ASN ** h 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 59092 Z= 0.233 Angle : 0.687 14.131 86264 Z= 0.345 Chirality : 0.038 0.258 10796 Planarity : 0.005 0.068 6060 Dihedral : 17.582 179.607 19667 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 1.00 % Allowed : 10.84 % Favored : 88.16 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 1.25 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.14), residues: 3387 helix: 0.34 (0.16), residues: 965 sheet: -1.90 (0.21), residues: 566 loop : -2.52 (0.13), residues: 1856 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 639 time to evaluate : 3.093 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 outliers start: 43 outliers final: 35 residues processed: 656 average time/residue: 0.5528 time to fit residues: 607.4759 Evaluate side-chains 625 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 590 time to evaluate : 4.174 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4217 time to fit residues: 31.0243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 409 optimal weight: 10.0000 chunk 431 optimal weight: 1.9990 chunk 393 optimal weight: 0.9980 chunk 419 optimal weight: 8.9990 chunk 252 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 329 optimal weight: 0.2980 chunk 128 optimal weight: 10.0000 chunk 379 optimal weight: 9.9990 chunk 396 optimal weight: 5.9990 chunk 417 optimal weight: 10.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS Q 118 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 ASN f 42 ASN ** h 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 420 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 59092 Z= 0.238 Angle : 0.692 14.191 86264 Z= 0.347 Chirality : 0.039 0.264 10796 Planarity : 0.005 0.069 6060 Dihedral : 17.575 179.508 19667 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.92 % Allowed : 11.37 % Favored : 87.72 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 0.62 % Twisted General : 0.03 % 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: -2.28 (0.14), residues: 3387 helix: 0.29 (0.17), residues: 960 sheet: -1.83 (0.21), residues: 569 loop : -2.49 (0.13), residues: 1858 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 646 time to evaluate : 3.132 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 outliers start: 45 outliers final: 34 residues processed: 666 average time/residue: 0.5416 time to fit residues: 606.8026 Evaluate side-chains 644 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 610 time to evaluate : 3.072 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4272 time to fit residues: 30.4197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 275 optimal weight: 2.9990 chunk 443 optimal weight: 5.9990 chunk 270 optimal weight: 0.0470 chunk 210 optimal weight: 5.9990 chunk 308 optimal weight: 7.9990 chunk 465 optimal weight: 4.9990 chunk 428 optimal weight: 7.9990 chunk 370 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 286 optimal weight: 0.8980 chunk 227 optimal weight: 7.9990 overall best weight: 2.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 79 ASN e 11 ASN ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 5 ASN ** h 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 59092 Z= 0.246 Angle : 0.706 14.229 86264 Z= 0.354 Chirality : 0.039 0.275 10796 Planarity : 0.005 0.072 6060 Dihedral : 17.573 179.932 19667 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.89 % Allowed : 11.28 % Favored : 87.84 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 1.25 % Twisted General : 0.03 % 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: -2.28 (0.14), residues: 3387 helix: 0.23 (0.16), residues: 965 sheet: -1.82 (0.21), residues: 552 loop : -2.47 (0.13), residues: 1870 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 632 time to evaluate : 3.097 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 outliers start: 21 outliers final: 13 residues processed: 638 average time/residue: 0.5635 time to fit residues: 603.2808 Evaluate side-chains 619 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 606 time to evaluate : 3.085 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3973 time to fit residues: 13.6300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 294 optimal weight: 10.0000 chunk 394 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 341 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 371 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 381 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 68 optimal weight: 30.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN ** W 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 79 ASN c 89 ASN ** d 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 ASN ** h 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.122202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096056 restraints weight = 130765.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.096600 restraints weight = 97046.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.097399 restraints weight = 67811.316| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.150 59092 Z= 0.551 Angle : 0.995 14.735 86264 Z= 0.494 Chirality : 0.051 0.370 10796 Planarity : 0.007 0.081 6060 Dihedral : 18.467 178.994 19667 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 25.89 Ramachandran Plot: Outliers : 0.89 % Allowed : 13.52 % Favored : 85.59 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 0.62 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.13), residues: 3387 helix: -0.70 (0.16), residues: 959 sheet: -2.19 (0.21), residues: 551 loop : -2.75 (0.13), residues: 1877 =============================================================================== Job complete usr+sys time: 11235.35 seconds wall clock time: 199 minutes 44.54 seconds (11984.54 seconds total)