Starting phenix.real_space_refine on Fri Dec 8 04:12:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/12_2023/5ll6_4071_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/12_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_4071/12_2023/5ll6_4071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/12_2023/5ll6_4071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/12_2023/5ll6_4071_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/12_2023/5ll6_4071_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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-1.21rc1-5172/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: 22.83, per 1000 atoms: 0.41 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: 20.75 Conformation dependent library (CDL) restraints added in 3.9 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: 20.74 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: 28.95 Time building geometry restraints manager: 22.55 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: 32580 35.83 - 71.66: 2796 71.66 - 107.49: 409 107.49 - 143.32: 28 143.32 - 179.15: 34 Dihedral angle restraints: 35847 sinusoidal: 25964 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 35844 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: 4.990 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: 13.590 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 140.380 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.130 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:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.590 ------------------------------------------------------------------------------- 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 : 22.778 179.146 29463 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 % Allowed : 7.37 % Favored : 90.10 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP a 83 HIS 0.011 0.003 HIS Y 123 PHE 0.053 0.004 PHE h 230 TYR 0.040 0.005 TYR X 97 ARG 0.023 0.002 ARG R 95 *********************** 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 : 3.001 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: 0.6544 time to fit residues: 1284.8760 Evaluate side-chains 726 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 712 time to evaluate : 3.013 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.4957 time to fit residues: 15.8965 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 ASN ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 59092 Z= 0.200 Angle : 0.736 12.919 86264 Z= 0.377 Chirality : 0.042 0.312 10796 Planarity : 0.006 0.076 6060 Dihedral : 23.158 179.674 22677 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 1.21 % Allowed : 9.77 % Favored : 89.02 % Rotamer: Outliers : 5.02 % Allowed : 19.11 % Favored : 75.87 % 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: -2.78 (0.13), residues: 3387 helix: 0.40 (0.17), residues: 968 sheet: -2.47 (0.18), residues: 585 loop : -3.02 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 230 HIS 0.007 0.001 HIS h 82 PHE 0.025 0.002 PHE d 58 TYR 0.024 0.002 TYR P 202 ARG 0.010 0.001 ARG X 99 *********************** 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 972 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 827 time to evaluate : 3.006 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 outliers start: 145 outliers final: 71 residues processed: 908 average time/residue: 0.5571 time to fit residues: 839.9358 Evaluate side-chains 745 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 674 time to evaluate : 2.979 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.4294 time to fit residues: 59.6625 ------------------------------------------------------------------------------- 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: 7.9990 chunk 131 optimal weight: 10.0000 chunk 352 optimal weight: 9.9990 chunk 288 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 458 optimal weight: 5.9990 chunk 378 optimal weight: 0.7980 chunk 421 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 340 optimal weight: 6.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 23 HIS 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 ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** d 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 HIS f 26 GLN g 17 GLN h 82 HIS h 228 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 59092 Z= 0.325 Angle : 0.769 13.853 86264 Z= 0.392 Chirality : 0.043 0.341 10796 Planarity : 0.006 0.105 6060 Dihedral : 23.100 179.278 22677 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 1.09 % Allowed : 10.81 % Favored : 88.10 % Rotamer: Outliers : 4.81 % Allowed : 21.91 % Favored : 73.28 % 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: -2.70 (0.13), residues: 3387 helix: 0.29 (0.16), residues: 952 sheet: -2.26 (0.19), residues: 585 loop : -2.89 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP c 136 HIS 0.007 0.002 HIS X 81 PHE 0.036 0.002 PHE S 205 TYR 0.030 0.003 TYR h 205 ARG 0.009 0.001 ARG a 62 *********************** 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 862 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 723 time to evaluate : 3.050 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 outliers start: 139 outliers final: 73 residues processed: 808 average time/residue: 0.5583 time to fit residues: 753.8701 Evaluate side-chains 705 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 632 time to evaluate : 2.954 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.3943 time to fit residues: 58.5214 ------------------------------------------------------------------------------- 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: 7.9990 chunk 319 optimal weight: 0.8980 chunk 220 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 202 optimal weight: 0.9990 chunk 285 optimal weight: 0.9980 chunk 426 optimal weight: 6.9990 chunk 451 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 404 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 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 b 15 ASN c 99 ASN d 106 GLN d 110 GLN g 17 GLN h 5 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 59092 Z= 0.222 Angle : 0.682 14.064 86264 Z= 0.346 Chirality : 0.039 0.303 10796 Planarity : 0.005 0.068 6060 Dihedral : 22.923 179.453 22677 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 1.03 % Allowed : 9.98 % Favored : 88.99 % Rotamer: Outliers : 3.53 % Allowed : 23.95 % Favored : 72.52 % 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: -2.50 (0.14), residues: 3387 helix: 0.39 (0.17), residues: 975 sheet: -2.12 (0.19), residues: 605 loop : -2.77 (0.13), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 29 HIS 0.013 0.001 HIS P 92 PHE 0.027 0.002 PHE P 38 TYR 0.036 0.002 TYR h 205 ARG 0.006 0.001 ARG Y 104 *********************** 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 811 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 709 time to evaluate : 3.002 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: 102 outliers final: 55 residues processed: 764 average time/residue: 0.5555 time to fit residues: 707.2456 Evaluate side-chains 675 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 620 time to evaluate : 3.011 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.4146 time to fit residues: 46.3976 ------------------------------------------------------------------------------- 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: 10.0000 chunk 256 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 385 optimal weight: 8.9990 chunk 312 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 chunk 405 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 83 GLN Q 101 HIS R 209 ASN ** R 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 123 HIS ** W 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 29 HIS b 39 GLN c 79 ASN d 110 GLN f 42 ASN ** f 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 59092 Z= 0.339 Angle : 0.783 14.162 86264 Z= 0.394 Chirality : 0.043 0.267 10796 Planarity : 0.006 0.070 6060 Dihedral : 23.042 179.482 22677 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 1.03 % Allowed : 11.34 % Favored : 87.63 % Rotamer: Outliers : 4.15 % Allowed : 25.75 % Favored : 70.09 % 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: -2.73 (0.13), residues: 3387 helix: -0.01 (0.16), residues: 973 sheet: -2.22 (0.19), residues: 620 loop : -2.79 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 230 HIS 0.010 0.002 HIS X 92 PHE 0.025 0.002 PHE f 79 TYR 0.036 0.002 TYR h 301 ARG 0.006 0.001 ARG a 62 *********************** 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 772 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 652 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 outliers start: 120 outliers final: 74 residues processed: 720 average time/residue: 0.5604 time to fit residues: 675.4720 Evaluate side-chains 671 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 597 time to evaluate : 3.030 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.4283 time to fit residues: 63.0016 ------------------------------------------------------------------------------- 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: 20.0000 chunk 406 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 451 optimal weight: 7.9990 chunk 375 optimal weight: 4.9990 chunk 209 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 101 HIS Q 160 HIS ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 180 GLN ** V 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 123 HIS ** W 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 ASN h 85 HIS h 213 ASN ** 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: 0.8164 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 59092 Z= 0.251 Angle : 0.703 14.231 86264 Z= 0.354 Chirality : 0.040 0.259 10796 Planarity : 0.005 0.068 6060 Dihedral : 22.900 178.321 22677 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 1.00 % Allowed : 10.16 % Favored : 88.84 % Rotamer: Outliers : 2.73 % Allowed : 27.17 % Favored : 70.09 % 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: -2.58 (0.14), residues: 3387 helix: 0.10 (0.16), residues: 979 sheet: -2.13 (0.21), residues: 577 loop : -2.69 (0.13), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Q 29 HIS 0.008 0.001 HIS U 89 PHE 0.047 0.002 PHE P 102 TYR 0.024 0.002 TYR h 205 ARG 0.008 0.001 ARG W 132 *********************** 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 755 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 676 time to evaluate : 4.062 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: 79 outliers final: 45 residues processed: 717 average time/residue: 0.5759 time to fit residues: 694.0500 Evaluate side-chains 652 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 607 time to evaluate : 2.974 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.4566 time to fit residues: 41.4927 ------------------------------------------------------------------------------- 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: 8.9990 chunk 50 optimal weight: 20.0000 chunk 257 optimal weight: 5.9990 chunk 329 optimal weight: 0.9980 chunk 255 optimal weight: 5.9990 chunk 380 optimal weight: 7.9990 chunk 252 optimal weight: 4.9990 chunk 450 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 274 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS S 209 HIS ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 123 HIS ** W 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 17 GLN h 213 ASN ** h 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 59092 Z= 0.355 Angle : 0.795 14.339 86264 Z= 0.398 Chirality : 0.043 0.291 10796 Planarity : 0.006 0.071 6060 Dihedral : 23.020 179.777 22677 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 1.00 % Allowed : 12.05 % Favored : 86.95 % Rotamer: Outliers : 2.98 % Allowed : 28.38 % Favored : 68.64 % 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: -2.73 (0.14), residues: 3387 helix: -0.11 (0.16), residues: 952 sheet: -2.23 (0.20), residues: 582 loop : -2.70 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Q 29 HIS 0.010 0.002 HIS W 123 PHE 0.033 0.002 PHE P 102 TYR 0.026 0.002 TYR h 301 ARG 0.007 0.001 ARG T 31 *********************** 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 717 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 631 time to evaluate : 3.010 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: 86 outliers final: 54 residues processed: 678 average time/residue: 0.5728 time to fit residues: 652.2746 Evaluate side-chains 644 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 590 time to evaluate : 3.006 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.4091 time to fit residues: 45.6530 ------------------------------------------------------------------------------- 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: 4.9990 chunk 179 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 286 optimal weight: 6.9990 chunk 306 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 353 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 HIS Q 101 HIS ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 123 HIS ** W 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 ASN c 89 ASN ** f 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 213 ASN ** h 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 59092 Z= 0.301 Angle : 0.749 14.361 86264 Z= 0.376 Chirality : 0.041 0.304 10796 Planarity : 0.005 0.072 6060 Dihedral : 22.945 179.869 22677 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.97 % Allowed : 11.72 % Favored : 87.30 % Rotamer: Outliers : 1.97 % Allowed : 29.60 % Favored : 68.43 % 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: -2.70 (0.14), residues: 3387 helix: -0.13 (0.16), residues: 966 sheet: -2.15 (0.21), residues: 574 loop : -2.69 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 29 HIS 0.008 0.001 HIS W 123 PHE 0.029 0.002 PHE P 102 TYR 0.023 0.002 TYR h 251 ARG 0.008 0.001 ARG a 62 *********************** 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 702 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 645 time to evaluate : 2.997 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: 57 outliers final: 34 residues processed: 673 average time/residue: 0.5523 time to fit residues: 629.1398 Evaluate side-chains 639 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 605 time to evaluate : 2.978 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4301 time to fit residues: 30.6848 ------------------------------------------------------------------------------- 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: 9.9990 chunk 431 optimal weight: 9.9990 chunk 393 optimal weight: 0.8980 chunk 419 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 329 optimal weight: 0.3980 chunk 128 optimal weight: 10.0000 chunk 379 optimal weight: 6.9990 chunk 396 optimal weight: 5.9990 chunk 417 optimal weight: 5.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 131 GLN ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 GLN e 80 HIS ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 315 ASN h 326 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 59092 Z= 0.230 Angle : 0.706 14.366 86264 Z= 0.354 Chirality : 0.039 0.293 10796 Planarity : 0.005 0.070 6060 Dihedral : 22.833 179.868 22677 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.92 % Allowed : 11.28 % Favored : 87.81 % Rotamer: Outliers : 1.32 % Allowed : 30.98 % Favored : 67.71 % 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: -2.50 (0.14), residues: 3387 helix: 0.09 (0.17), residues: 957 sheet: -2.08 (0.21), residues: 569 loop : -2.58 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Q 29 HIS 0.009 0.001 HIS P 92 PHE 0.028 0.002 PHE P 102 TYR 0.024 0.002 TYR R 222 ARG 0.008 0.001 ARG a 62 *********************** 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 687 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 649 time to evaluate : 2.999 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: 38 outliers final: 31 residues processed: 662 average time/residue: 0.5555 time to fit residues: 619.1337 Evaluate side-chains 642 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 611 time to evaluate : 3.249 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4071 time to fit residues: 27.8231 ------------------------------------------------------------------------------- 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: 10.0000 chunk 443 optimal weight: 7.9990 chunk 270 optimal weight: 0.3980 chunk 210 optimal weight: 6.9990 chunk 308 optimal weight: 6.9990 chunk 465 optimal weight: 2.9990 chunk 428 optimal weight: 5.9990 chunk 370 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 286 optimal weight: 3.9990 chunk 227 optimal weight: 0.5980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 GLN ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 59092 Z= 0.238 Angle : 0.713 14.392 86264 Z= 0.357 Chirality : 0.039 0.291 10796 Planarity : 0.005 0.070 6060 Dihedral : 22.800 179.816 22677 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.89 % Allowed : 11.37 % Favored : 87.75 % Rotamer: Outliers : 0.45 % Allowed : 31.74 % Favored : 67.81 % 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: -2.44 (0.14), residues: 3387 helix: 0.12 (0.17), residues: 957 sheet: -2.03 (0.21), residues: 560 loop : -2.52 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Q 29 HIS 0.011 0.001 HIS P 92 PHE 0.045 0.002 PHE U 169 TYR 0.038 0.002 TYR a 12 ARG 0.010 0.001 ARG U 114 ********************** 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 639 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 626 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 outliers start: 13 outliers final: 8 residues processed: 632 average time/residue: 0.5795 time to fit residues: 613.4744 Evaluate side-chains 612 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 604 time to evaluate : 3.030 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5079 time to fit residues: 10.7249 ------------------------------------------------------------------------------- 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: 7.9990 chunk 394 optimal weight: 0.0170 chunk 113 optimal weight: 10.0000 chunk 341 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 371 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 381 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 68 optimal weight: 30.0000 overall best weight: 5.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 GLN Y 105 ASN ** b 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 326 ASN ** h 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.124277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.098211 restraints weight = 129325.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.099102 restraints weight = 89050.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.099774 restraints weight = 59840.293| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 59092 Z= 0.417 Angle : 0.861 14.604 86264 Z= 0.430 Chirality : 0.045 0.336 10796 Planarity : 0.006 0.073 6060 Dihedral : 23.047 179.944 22677 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.92 % Allowed : 12.78 % Favored : 86.30 % Rotamer: Outliers : 1.14 % Allowed : 32.23 % Favored : 66.63 % 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: -2.86 (0.14), residues: 3387 helix: -0.38 (0.16), residues: 955 sheet: -2.28 (0.20), residues: 573 loop : -2.68 (0.13), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP Q 29 HIS 0.009 0.002 HIS X 92 PHE 0.039 0.003 PHE S 205 TYR 0.042 0.003 TYR R 222 ARG 0.008 0.001 ARG b 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11534.24 seconds wall clock time: 205 minutes 4.68 seconds (12304.68 seconds total)