Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 13:26:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etj_24396/04_2023/8etj_24396.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etj_24396/04_2023/8etj_24396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etj_24396/04_2023/8etj_24396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etj_24396/04_2023/8etj_24396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etj_24396/04_2023/8etj_24396.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etj_24396/04_2023/8etj_24396.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1961 5.49 5 S 99 5.16 5 C 42587 2.51 5 N 14882 2.21 5 O 20327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "C ASP 14": "OD1" <-> "OD2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 33": "OE1" <-> "OE2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 234": "OD1" <-> "OD2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 156": "OD1" <-> "OD2" Residue "H GLU 9": "OE1" <-> "OE2" Residue "H TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 140": "OD1" <-> "OD2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H ASP 169": "OD1" <-> "OD2" Residue "H TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 107": "OD1" <-> "OD2" Residue "M PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 122": "OE1" <-> "OE2" Residue "N GLU 8": "OE1" <-> "OE2" Residue "N ASP 17": "OD1" <-> "OD2" Residue "N TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 11": "OD1" <-> "OD2" Residue "O GLU 107": "OE1" <-> "OE2" Residue "O PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 184": "OE1" <-> "OE2" Residue "P GLU 53": "OE1" <-> "OE2" Residue "P TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 99": "OE1" <-> "OE2" Residue "P GLU 152": "OE1" <-> "OE2" Residue "Q GLU 21": "OE1" <-> "OE2" Residue "S ASP 95": "OD1" <-> "OD2" Residue "V TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 58": "OD1" <-> "OD2" Residue "V ASP 91": "OD1" <-> "OD2" Residue "V GLU 98": "OE1" <-> "OE2" Residue "V ASP 99": "OD1" <-> "OD2" Residue "Y GLU 87": "OE1" <-> "OE2" Residue "Y ASP 99": "OD1" <-> "OD2" Residue "a GLU 135": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "b TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 60": "OE1" <-> "OE2" Residue "b PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 112": "OD1" <-> "OD2" Residue "b TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 392": "OD1" <-> "OD2" Residue "b TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 418": "OD1" <-> "OD2" Residue "b TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 437": "OD1" <-> "OD2" Residue "b PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 57": "OD1" <-> "OD2" Residue "e GLU 27": "OE1" <-> "OE2" Residue "e GLU 80": "OE1" <-> "OE2" Residue "e GLU 107": "OE1" <-> "OE2" Residue "h GLU 14": "OE1" <-> "OE2" Residue "h GLU 18": "OE1" <-> "OE2" Residue "h GLU 22": "OE1" <-> "OE2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "h GLU 70": "OE1" <-> "OE2" Residue "h ASP 81": "OD1" <-> "OD2" Residue "i PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 57": "OE1" <-> "OE2" Residue "i GLU 87": "OE1" <-> "OE2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r GLU 57": "OE1" <-> "OE2" Residue "r GLU 69": "OE1" <-> "OE2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "u ASP 25": "OD1" <-> "OD2" Residue "u ASP 83": "OD1" <-> "OD2" Residue "u GLU 105": "OE1" <-> "OE2" Residue "T PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 144": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 79857 Number of models: 1 Model: "" Number of chains: 36 Chain: "1" Number of atoms: 38913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1817, 38913 Classifications: {'RNA': 1817} Modifications used: {'rna2p_pur': 191, 'rna2p_pyr': 124, 'rna3p_pur': 839, 'rna3p_pyr': 663} Link IDs: {'rna2p': 314, 'rna3p': 1502} Chain breaks: 23 Chain: "2" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 3069 Classifications: {'RNA': 144} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 8, 'rna3p_pur': 62, 'rna3p_pyr': 59} Link IDs: {'rna2p': 23, 'rna3p': 120} Chain breaks: 3 Chain: "3" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1042 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "B" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2662 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2553 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 307} Chain breaks: 1 Chain: "E" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1283 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Chain: "F" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 206} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1307 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1291 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 160} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 168, 1291 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 160} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1290 Chain: "H" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1451 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "L" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1427 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "M" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1007 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "N" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1406 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 2 Chain: "O" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain: "P" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 2 Chain: "Q" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1032 Classifications: {'peptide': 133} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 278 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 84 Chain: "S" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1408 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain breaks: 1 Chain: "V" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1026 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "W" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1057 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 8, 'TRANS': 206} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 670 Unresolved non-hydrogen angles: 855 Unresolved non-hydrogen dihedrals: 564 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 13, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 346 Chain: "Y" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "a" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 747 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain breaks: 1 Chain: "b" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2837 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 17, 'TRANS': 397} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 512 Unresolved non-hydrogen angles: 660 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 246 Chain: "d" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 810 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "e" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 944 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "f" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 839 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 999 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "i" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 748 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "j" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 563 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 68} Chain: "r" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1086 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 119 Chain: "s" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 257 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "u" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 944 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "w" Number of atoms: 521 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 104, 516 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 3, 'TRANS': 100} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 198 Conformer: "B" Number of residues, atoms: 104, 516 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 3, 'TRANS': 100} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 198 bond proxies already assigned to first conformer: 509 Chain: "y" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1697 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "z" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 292 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "T" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 126 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 2, 'TRANS': 13} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 74416 SG CYS j 19 102.156 110.610 169.175 1.00 64.08 S ATOM 74444 SG CYS j 22 104.321 111.786 166.256 1.00 65.72 S ATOM 74540 SG CYS j 34 103.712 108.119 166.669 1.00 70.97 S ATOM 74557 SG CYS j 37 105.785 109.789 169.278 1.00 62.80 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AASN G 182 " occ=0.62 ... (14 atoms not shown) pdb=" ND2BASN G 182 " occ=0.38 residue: pdb=" N AASP G 227 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP G 227 " occ=0.50 residue: pdb=" N AGLU w 243 " occ=0.50 ... (8 atoms not shown) pdb=" CB BGLU w 243 " occ=0.50 Time building chain proxies: 31.59, per 1000 atoms: 0.40 Number of scatterers: 79857 At special positions: 0 Unit cell: (217.3, 178.08, 256.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 99 16.00 P 1961 15.00 O 20327 8.00 N 14882 7.00 C 42587 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: 33.87 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " Number of angles added : 6 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9394 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 57 sheets defined 43.2% alpha, 14.2% beta 586 base pairs and 1132 stacking pairs defined. Time for finding SS restraints: 24.93 Creating SS restraints... Processing helix chain '3' and resid 3 through 12 Processing helix chain '3' and resid 72 through 77 removed outlier: 4.558A pdb=" N TRP 3 77 " --> pdb=" O PRO 3 73 " (cutoff:3.500A) Processing helix chain '3' and resid 85 through 96 Processing helix chain '3' and resid 104 through 124 removed outlier: 3.752A pdb=" N GLN 3 110 " --> pdb=" O HIS 3 106 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR 3 113 " --> pdb=" O LYS 3 109 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG 3 114 " --> pdb=" O GLN 3 110 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU 3 119 " --> pdb=" O LEU 3 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 removed outlier: 4.035A pdb=" N PHE B 16 " --> pdb=" O SER B 13 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 17 " --> pdb=" O LEU B 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 13 through 17' Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 141 through 155 Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 46 through 49 removed outlier: 3.738A pdb=" N ARG C 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 46 through 49' Processing helix chain 'C' and resid 116 through 131 Processing helix chain 'C' and resid 133 through 141 Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 194 through 198 removed outlier: 4.095A pdb=" N ASN C 198 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 241 through 245 Processing helix chain 'C' and resid 254 through 265 removed outlier: 4.872A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER C 262 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 323 through 331 removed outlier: 3.576A pdb=" N LEU C 327 " --> pdb=" O ASN C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 removed outlier: 4.186A pdb=" N TYR C 337 " --> pdb=" O ALA C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.996A pdb=" N PHE E 65 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 150 through 171 removed outlier: 3.902A pdb=" N ILE E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) Proline residue: E 166 - end of helix removed outlier: 3.709A pdb=" N ILE E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'F' and resid 36 through 80 Processing helix chain 'F' and resid 103 through 114 Processing helix chain 'F' and resid 127 through 135 removed outlier: 3.708A pdb=" N GLN F 135 " --> pdb=" O LYS F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 147 through 159 removed outlier: 3.512A pdb=" N VAL F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 181 removed outlier: 4.112A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA F 179 " --> pdb=" O ILE F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 187 through 197 Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 202 through 207 removed outlier: 3.565A pdb=" N ALA F 206 " --> pdb=" O PHE F 202 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN F 207 " --> pdb=" O LYS F 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 202 through 207' Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.523A pdb=" N GLY F 232 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 241 No H-bonds generated for 'chain 'F' and resid 239 through 241' Processing helix chain 'F' and resid 242 through 250 Processing helix chain 'G' and resid 63 through 69 removed outlier: 3.678A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 removed outlier: 5.113A pdb=" N PHE G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 96 removed outlier: 3.713A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 118 Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 190 removed outlier: 4.054A pdb=" N LEU G 186 " --> pdb=" O AASN G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 222 removed outlier: 4.116A pdb=" N ASN G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 227 Processing helix chain 'H' and resid 21 through 23 No H-bonds generated for 'chain 'H' and resid 21 through 23' Processing helix chain 'H' and resid 61 through 66 Processing helix chain 'H' and resid 66 through 84 removed outlier: 3.815A pdb=" N SER H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 Processing helix chain 'H' and resid 148 through 163 removed outlier: 3.528A pdb=" N CYS H 163 " --> pdb=" O ILE H 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 93 removed outlier: 3.882A pdb=" N SER L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.575A pdb=" N ASN L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG L 115 " --> pdb=" O ARG L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 removed outlier: 3.996A pdb=" N GLY L 131 " --> pdb=" O PRO L 127 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN L 132 " --> pdb=" O ARG L 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 132' Processing helix chain 'L' and resid 148 through 153 removed outlier: 3.645A pdb=" N VAL L 152 " --> pdb=" O ASP L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 173 Processing helix chain 'L' and resid 175 through 200 removed outlier: 4.456A pdb=" N ASN L 181 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY L 190 " --> pdb=" O ALA L 186 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA L 191 " --> pdb=" O ARG L 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 90 through 104 Processing helix chain 'M' and resid 106 through 122 Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.841A pdb=" N LEU N 7 " --> pdb=" O ALA N 3 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU N 8 " --> pdb=" O TYR N 4 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU N 9 " --> pdb=" O LYS N 5 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.509A pdb=" N ARG N 24 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 removed outlier: 3.717A pdb=" N ARG N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 152 Processing helix chain 'N' and resid 153 through 157 removed outlier: 3.579A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'O' and resid 16 through 30 removed outlier: 3.624A pdb=" N VAL O 23 " --> pdb=" O ARG O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 41 removed outlier: 3.649A pdb=" N GLU O 41 " --> pdb=" O ARG O 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 38 through 41' Processing helix chain 'O' and resid 47 through 59 removed outlier: 3.681A pdb=" N TYR O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 88 Processing helix chain 'O' and resid 93 through 101 Processing helix chain 'O' and resid 125 through 130 Processing helix chain 'O' and resid 139 through 144 Processing helix chain 'O' and resid 150 through 186 Processing helix chain 'O' and resid 187 through 196 removed outlier: 3.921A pdb=" N SER O 193 " --> pdb=" O GLN O 190 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLN O 194 " --> pdb=" O LYS O 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 36 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 74 Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.541A pdb=" N VAL P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.707A pdb=" N LEU P 112 " --> pdb=" O MET P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 183 removed outlier: 3.793A pdb=" N ALA P 183 " --> pdb=" O ALA P 179 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 52 removed outlier: 3.511A pdb=" N LYS Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 58 Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 108 through 118 removed outlier: 3.757A pdb=" N ALA Q 118 " --> pdb=" O ARG Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 132 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 35 Processing helix chain 'R' and resid 37 through 48 Processing helix chain 'S' and resid 32 through 49 Processing helix chain 'S' and resid 97 through 113 Processing helix chain 'S' and resid 130 through 134 Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'V' and resid 122 through 128 Processing helix chain 'V' and resid 128 through 134 Processing helix chain 'W' and resid 19 through 35 Processing helix chain 'W' and resid 49 through 59 removed outlier: 3.661A pdb=" N LEU W 53 " --> pdb=" O ARG W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 78 Processing helix chain 'W' and resid 88 through 96 removed outlier: 3.632A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS W 94 " --> pdb=" O SER W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'W' and resid 161 through 169 removed outlier: 3.532A pdb=" N VAL W 165 " --> pdb=" O LEU W 161 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG W 166 " --> pdb=" O GLU W 162 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY W 169 " --> pdb=" O VAL W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 195 through 204 removed outlier: 3.697A pdb=" N LEU W 204 " --> pdb=" O ARG W 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 20 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 4.574A pdb=" N VAL Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 74 through 77 Processing helix chain 'Y' and resid 99 through 101 No H-bonds generated for 'chain 'Y' and resid 99 through 101' Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'a' and resid 7 through 11 Processing helix chain 'a' and resid 77 through 81 Processing helix chain 'a' and resid 83 through 91 Processing helix chain 'a' and resid 104 through 107 Processing helix chain 'a' and resid 132 through 140 removed outlier: 3.716A pdb=" N ILE a 137 " --> pdb=" O ALA a 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 9 removed outlier: 4.114A pdb=" N ASN b 8 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE b 9 " --> pdb=" O PHE b 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 5 through 9' Processing helix chain 'b' and resid 15 through 30 Processing helix chain 'b' and resid 39 through 69 Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.585A pdb=" N ILE b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 118 removed outlier: 3.568A pdb=" N LYS b 118 " --> pdb=" O ILE b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 143 removed outlier: 3.720A pdb=" N ARG b 143 " --> pdb=" O THR b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 159 Processing helix chain 'b' and resid 180 through 189 Processing helix chain 'b' and resid 235 through 246 removed outlier: 3.546A pdb=" N HIS b 246 " --> pdb=" O THR b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 276 Processing helix chain 'b' and resid 306 through 312 Processing helix chain 'b' and resid 328 through 344 Processing helix chain 'b' and resid 379 through 384 removed outlier: 3.588A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR b 384 " --> pdb=" O ASP b 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 379 through 384' Processing helix chain 'b' and resid 398 through 406 Processing helix chain 'b' and resid 415 through 420 removed outlier: 4.025A pdb=" N LYS b 419 " --> pdb=" O LEU b 416 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR b 420 " --> pdb=" O ARG b 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 426 through 430 removed outlier: 3.574A pdb=" N TYR b 429 " --> pdb=" O SER b 426 " (cutoff:3.500A) Processing helix chain 'b' and resid 442 through 445 Processing helix chain 'b' and resid 448 through 465 removed outlier: 3.747A pdb=" N GLU b 458 " --> pdb=" O LEU b 454 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU b 459 " --> pdb=" O ALA b 455 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 25 Processing helix chain 'd' and resid 29 through 31 No H-bonds generated for 'chain 'd' and resid 29 through 31' Processing helix chain 'd' and resid 32 through 50 Processing helix chain 'd' and resid 57 through 65 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 75 through 81 removed outlier: 3.892A pdb=" N VAL e 79 " --> pdb=" O ASN e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 86 removed outlier: 3.855A pdb=" N ASN e 86 " --> pdb=" O LEU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 98 through 113 Processing helix chain 'f' and resid 38 through 43 Processing helix chain 'f' and resid 91 through 95 removed outlier: 3.800A pdb=" N PHE f 95 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 9 removed outlier: 3.529A pdb=" N LEU h 8 " --> pdb=" O LYS h 4 " (cutoff:3.500A) Processing helix chain 'h' and resid 12 through 36 removed outlier: 3.540A pdb=" N GLU h 26 " --> pdb=" O GLU h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 39 through 72 removed outlier: 4.418A pdb=" N LYS h 47 " --> pdb=" O LEU h 43 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR h 48 " --> pdb=" O SER h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 93 Processing helix chain 'h' and resid 95 through 100 Processing helix chain 'h' and resid 103 through 113 Processing helix chain 'i' and resid 23 through 28 Processing helix chain 'i' and resid 32 through 47 Processing helix chain 'i' and resid 49 through 61 removed outlier: 3.870A pdb=" N GLU i 57 " --> pdb=" O ARG i 53 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU i 58 " --> pdb=" O ARG i 54 " (cutoff:3.500A) Processing helix chain 'i' and resid 63 through 76 Processing helix chain 'i' and resid 77 through 95 removed outlier: 3.534A pdb=" N GLU i 87 " --> pdb=" O GLY i 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 Processing helix chain 'j' and resid 64 through 75 removed outlier: 3.643A pdb=" N LYS j 69 " --> pdb=" O SER j 65 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS j 75 " --> pdb=" O HIS j 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 19 through 42 removed outlier: 3.636A pdb=" N GLU r 31 " --> pdb=" O LYS r 27 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA r 32 " --> pdb=" O ALA r 28 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR r 42 " --> pdb=" O TYR r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 73 removed outlier: 3.651A pdb=" N GLU r 69 " --> pdb=" O ILE r 65 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU r 70 " --> pdb=" O LYS r 66 " (cutoff:3.500A) Processing helix chain 'r' and resid 205 through 212 Processing helix chain 'r' and resid 247 through 252 Processing helix chain 's' and resid 12 through 32 removed outlier: 4.617A pdb=" N GLU s 20 " --> pdb=" O ARG s 16 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS s 21 " --> pdb=" O SER s 17 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 45 through 49 removed outlier: 3.591A pdb=" N VAL u 49 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 59 Processing helix chain 'u' and resid 67 through 71 Processing helix chain 'u' and resid 83 through 114 removed outlier: 3.629A pdb=" N LYS u 95 " --> pdb=" O LEU u 91 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN u 99 " --> pdb=" O LYS u 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU u 107 " --> pdb=" O LYS u 103 " (cutoff:3.500A) Processing helix chain 'w' and resid 227 through 234 removed outlier: 4.026A pdb=" N LYS w 231 " --> pdb=" O ASN w 227 " (cutoff:3.500A) Processing helix chain 'w' and resid 258 through 264 Processing helix chain 'w' and resid 266 through 274 Processing helix chain 'w' and resid 283 through 292 Processing helix chain 'w' and resid 296 through 305 removed outlier: 4.023A pdb=" N ASP w 305 " --> pdb=" O LEU w 301 " (cutoff:3.500A) Processing helix chain 'w' and resid 310 through 329 Processing helix chain 'y' and resid 31 through 43 removed outlier: 3.757A pdb=" N TYR y 35 " --> pdb=" O SER y 31 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU y 41 " --> pdb=" O VAL y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 107 removed outlier: 3.568A pdb=" N ILE y 107 " --> pdb=" O ALA y 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 103 through 107' Processing helix chain 'y' and resid 122 through 134 Processing helix chain 'y' and resid 147 through 152 Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 196 Processing helix chain 'y' and resid 211 through 223 Processing helix chain 'z' and resid 88 through 99 Processing helix chain 'z' and resid 101 through 116 removed outlier: 4.371A pdb=" N ASN z 107 " --> pdb=" O LYS z 103 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE z 110 " --> pdb=" O LYS z 106 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS z 112 " --> pdb=" O SER z 108 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU z 114 " --> pdb=" O PHE z 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '3' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain '3' and resid 52 through 56 removed outlier: 3.635A pdb=" N MET 3 64 " --> pdb=" O GLN 3 78 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN 3 78 " --> pdb=" O MET 3 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.318A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.318A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.680A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE B 359 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N HIS B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL B 220 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL B 217 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU B 278 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLY B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N THR B 276 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS B 281 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE B 321 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 223 through 225 Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 23 removed outlier: 5.110A pdb=" N ILE C 10 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLU C 20 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL C 8 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL C 153 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU C 152 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 208 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR C 253 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL C 210 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL C 209 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AA9, first strand: chain 'E' and resid 94 through 97 removed outlier: 7.115A pdb=" N THR E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLN E 75 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 81 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 82 through 83 Processing sheet with id=AB2, first strand: chain 'F' and resid 122 through 125 removed outlier: 3.566A pdb=" N ILE F 91 " --> pdb=" O VAL F 124 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL F 141 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AB4, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AB5, first strand: chain 'H' and resid 6 through 12 Processing sheet with id=AB6, first strand: chain 'H' and resid 18 through 20 removed outlier: 4.008A pdb=" N ASP H 20 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.667A pdb=" N ARG H 87 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG H 182 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS H 89 " --> pdb=" O SER H 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AB9, first strand: chain 'L' and resid 22 through 24 Processing sheet with id=AC1, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AC2, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AC3, first strand: chain 'M' and resid 49 through 52 removed outlier: 7.677A pdb=" N ARG M 36 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE M 31 " --> pdb=" O ARG M 36 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU M 38 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL M 13 " --> pdb=" O THR M 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.474A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 7 through 11 removed outlier: 6.059A pdb=" N VAL O 8 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL O 37 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE O 10 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AC7, first strand: chain 'P' and resid 15 through 22 removed outlier: 3.890A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA P 151 " --> pdb=" O ILE P 114 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE P 114 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AC9, first strand: chain 'Q' and resid 61 through 62 Processing sheet with id=AD1, first strand: chain 'Q' and resid 121 through 123 removed outlier: 6.433A pdb=" N ILE Q 102 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR Q 82 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL Q 139 " --> pdb=" O THR Q 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AD3, first strand: chain 'S' and resid 55 through 63 removed outlier: 5.095A pdb=" N ILE S 57 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG S 11 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU S 5 " --> pdb=" O ILE S 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 87 through 95 removed outlier: 4.311A pdb=" N VAL S 73 " --> pdb=" O VAL S 128 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG S 79 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE S 122 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'V' and resid 19 through 20 Processing sheet with id=AD6, first strand: chain 'V' and resid 24 through 27 removed outlier: 6.839A pdb=" N LEU V 61 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL V 41 " --> pdb=" O MET V 59 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N MET V 59 " --> pdb=" O VAL V 41 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP V 58 " --> pdb=" O VAL V 80 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLY V 102 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN V 26 " --> pdb=" O GLY V 102 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE V 104 " --> pdb=" O ASN V 26 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 87 through 88 Processing sheet with id=AD8, first strand: chain 'V' and resid 119 through 121 removed outlier: 5.828A pdb=" N VAL V 120 " --> pdb=" O VAL V 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'W' and resid 135 through 137 removed outlier: 6.360A pdb=" N ILE W 137 " --> pdb=" O PRO W 186 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'W' and resid 140 through 141 Processing sheet with id=AE2, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AE3, first strand: chain 'Y' and resid 93 through 98 removed outlier: 7.007A pdb=" N VAL Y 84 " --> pdb=" O VAL Y 96 " (cutoff:3.500A) removed outlier: 10.849A pdb=" N ILE Y 98 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 10.680A pdb=" N GLU Y 82 " --> pdb=" O ILE Y 98 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER Y 71 " --> pdb=" O LEU Y 80 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU Y 82 " --> pdb=" O ILE Y 69 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE Y 69 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N VAL Y 84 " --> pdb=" O GLY Y 67 " (cutoff:3.500A) removed outlier: 10.019A pdb=" N GLY Y 67 " --> pdb=" O VAL Y 84 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN Y 54 " --> pdb=" O THR Y 106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'a' and resid 72 through 74 removed outlier: 5.905A pdb=" N VAL a 73 " --> pdb=" O LEU a 112 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'a' and resid 100 through 102 removed outlier: 6.315A pdb=" N ILE a 101 " --> pdb=" O GLN a 125 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL a 124 " --> pdb=" O GLU a 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'b' and resid 206 through 212 Processing sheet with id=AE7, first strand: chain 'b' and resid 254 through 256 Processing sheet with id=AE8, first strand: chain 'b' and resid 435 through 436 Processing sheet with id=AE9, first strand: chain 'd' and resid 55 through 56 Processing sheet with id=AF1, first strand: chain 'e' and resid 69 through 73 Processing sheet with id=AF2, first strand: chain 'f' and resid 9 through 19 removed outlier: 6.892A pdb=" N ILE f 30 " --> pdb=" O LEU f 15 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N PHE f 17 " --> pdb=" O THR f 28 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR f 28 " --> pdb=" O PHE f 17 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N ARG f 19 " --> pdb=" O PRO f 26 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA f 81 " --> pdb=" O PRO f 75 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG f 83 " --> pdb=" O ALA f 73 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL f 60 " --> pdb=" O SER f 63 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE f 65 " --> pdb=" O LYS f 58 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N LYS f 58 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N VAL f 67 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N SER f 56 " --> pdb=" O VAL f 67 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N TRP f 69 " --> pdb=" O TYR f 54 " (cutoff:3.500A) removed outlier: 11.470A pdb=" N TYR f 54 " --> pdb=" O TRP f 69 " (cutoff:3.500A) removed outlier: 10.942A pdb=" N THR f 71 " --> pdb=" O TYR f 52 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N TYR f 52 " --> pdb=" O THR f 71 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N ALA f 73 " --> pdb=" O VAL f 50 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N VAL f 50 " --> pdb=" O ALA f 73 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG f 49 " --> pdb=" O MET f 102 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL f 53 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER f 98 " --> pdb=" O VAL f 53 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'j' and resid 16 through 18 Processing sheet with id=AF4, first strand: chain 'r' and resid 180 through 184 removed outlier: 6.545A pdb=" N VAL r 219 " --> pdb=" O LYS r 200 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'u' and resid 4 through 5 removed outlier: 3.523A pdb=" N HIS u 4 " --> pdb=" O VAL u 13 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'u' and resid 19 through 22 Processing sheet with id=AF7, first strand: chain 'w' and resid 255 through 257 removed outlier: 6.084A pdb=" N VAL w 256 " --> pdb=" O VAL w 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'y' and resid 3 through 4 removed outlier: 5.883A pdb=" N LEU y 3 " --> pdb=" O ALA y 206 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.408A pdb=" N ALA y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'y' and resid 64 through 65 Processing sheet with id=AG2, first strand: chain 'y' and resid 108 through 110 Processing sheet with id=AG3, first strand: chain 'y' and resid 153 through 154 removed outlier: 6.230A pdb=" N ALA y 159 " --> pdb=" O VAL y 182 " (cutoff:3.500A) 1648 hydrogen bonds defined for protein. 4638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1435 hydrogen bonds 2330 hydrogen bond angles 0 basepair planarities 586 basepair parallelities 1132 stacking parallelities Total time for adding SS restraints: 69.46 Time building geometry restraints manager: 36.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13229 1.33 - 1.45: 32556 1.45 - 1.58: 35611 1.58 - 1.70: 3894 1.70 - 1.83: 156 Bond restraints: 85446 Sorted by residual: bond pdb=" CA PRO F 103 " pdb=" C PRO F 103 " ideal model delta sigma weight residual 1.514 1.528 -0.014 5.50e-03 3.31e+04 6.32e+00 bond pdb=" CA TRP N 120 " pdb=" C TRP N 120 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.25e-02 6.40e+03 3.90e+00 bond pdb=" N LYS C 347 " pdb=" CA LYS C 347 " ideal model delta sigma weight residual 1.455 1.431 0.024 1.25e-02 6.40e+03 3.76e+00 bond pdb=" O3' A 13267 " pdb=" P U 13268 " ideal model delta sigma weight residual 1.607 1.634 -0.027 1.50e-02 4.44e+03 3.26e+00 bond pdb=" CA TYR H 6 " pdb=" C TYR H 6 " ideal model delta sigma weight residual 1.526 1.504 0.022 1.20e-02 6.94e+03 3.25e+00 ... (remaining 85441 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.39: 9674 105.39 - 112.62: 48737 112.62 - 119.86: 30071 119.86 - 127.10: 31748 127.10 - 134.34: 4762 Bond angle restraints: 124992 Sorted by residual: angle pdb=" N ILE b 12 " pdb=" CA ILE b 12 " pdb=" C ILE b 12 " ideal model delta sigma weight residual 108.63 115.30 -6.67 8.60e-01 1.35e+00 6.01e+01 angle pdb=" N TYR H 6 " pdb=" CA TYR H 6 " pdb=" C TYR H 6 " ideal model delta sigma weight residual 107.70 120.34 -12.64 2.09e+00 2.29e-01 3.65e+01 angle pdb=" C4' U 1 270 " pdb=" C3' U 1 270 " pdb=" O3' U 1 270 " ideal model delta sigma weight residual 109.40 116.92 -7.52 1.50e+00 4.44e-01 2.51e+01 angle pdb=" O3' U 13268 " pdb=" C3' U 13268 " pdb=" C2' U 13268 " ideal model delta sigma weight residual 109.50 116.93 -7.43 1.50e+00 4.44e-01 2.45e+01 angle pdb=" CA GLU E 33 " pdb=" CB GLU E 33 " pdb=" CG GLU E 33 " ideal model delta sigma weight residual 114.10 123.88 -9.78 2.00e+00 2.50e-01 2.39e+01 ... (remaining 124987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 45134 35.96 - 71.93: 1798 71.93 - 107.89: 203 107.89 - 143.86: 31 143.86 - 179.82: 43 Dihedral angle restraints: 47209 sinusoidal: 32744 harmonic: 14465 Sorted by residual: dihedral pdb=" O4' U 11330 " pdb=" C1' U 11330 " pdb=" N1 U 11330 " pdb=" C2 U 11330 " ideal model delta sinusoidal sigma weight residual -160.00 19.82 -179.82 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 2 164 " pdb=" C1' U 2 164 " pdb=" N1 U 2 164 " pdb=" C2 U 2 164 " ideal model delta sinusoidal sigma weight residual 200.00 21.56 178.44 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 1 140 " pdb=" C1' U 1 140 " pdb=" N1 U 1 140 " pdb=" C2 U 1 140 " ideal model delta sinusoidal sigma weight residual -160.00 16.32 -176.32 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 47206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 15573 0.130 - 0.260: 79 0.260 - 0.390: 5 0.390 - 0.521: 0 0.521 - 0.651: 1 Chirality restraints: 15658 Sorted by residual: chirality pdb=" CG LEU b 456 " pdb=" CB LEU b 456 " pdb=" CD1 LEU b 456 " pdb=" CD2 LEU b 456 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CG LEU u 69 " pdb=" CB LEU u 69 " pdb=" CD1 LEU u 69 " pdb=" CD2 LEU u 69 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C3' C 1 626 " pdb=" C4' C 1 626 " pdb=" O3' C 1 626 " pdb=" C2' C 1 626 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 15655 not shown) Planarity restraints: 8644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR b 10 " 0.053 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO b 11 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO b 11 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO b 11 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY i 4 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C GLY i 4 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY i 4 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU i 5 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 118 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C ASN G 118 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN G 118 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY G 119 " 0.015 2.00e-02 2.50e+03 ... (remaining 8641 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 1793 2.63 - 3.20: 70218 3.20 - 3.76: 154614 3.76 - 4.33: 206583 4.33 - 4.90: 285803 Nonbonded interactions: 719011 Sorted by model distance: nonbonded pdb=" O ASP M 82 " pdb=" OD1 ASP M 82 " model vdw 2.061 3.040 nonbonded pdb=" O2' C 11308 " pdb=" O5' A 11309 " model vdw 2.106 2.440 nonbonded pdb=" O2' G 13387 " pdb=" O5' C 13388 " model vdw 2.155 2.440 nonbonded pdb=" N GLU T 144 " pdb=" OE1 GLU T 144 " model vdw 2.172 2.520 nonbonded pdb=" N GLN O 190 " pdb=" OE1 GLN O 190 " model vdw 2.177 2.520 ... (remaining 719006 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 30.130 Check model and map are aligned: 0.910 Set scattering table: 0.530 Process input model: 235.420 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.230 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 279.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.004 0.072 85446 Z= 0.230 Angle : 0.606 12.635 124992 Z= 0.322 Chirality : 0.036 0.651 15658 Planarity : 0.005 0.079 8644 Dihedral : 17.199 179.822 37815 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.90 % Favored : 94.91 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.12), residues: 4886 helix: 0.17 (0.12), residues: 1856 sheet: -0.73 (0.21), residues: 597 loop : -1.03 (0.13), residues: 2433 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 682 time to evaluate : 4.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 693 average time/residue: 0.7928 time to fit residues: 937.4065 Evaluate side-chains 610 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 597 time to evaluate : 4.454 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.7462 time to fit residues: 21.7614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 571 optimal weight: 0.9990 chunk 513 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 530 optimal weight: 2.9990 chunk 205 optimal weight: 8.9990 chunk 322 optimal weight: 0.9990 chunk 394 optimal weight: 1.9990 chunk 614 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN E 127 GLN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 ASN ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 HIS Q 78 GLN ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 394 ASN h 11 GLN ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN ** r 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN y 168 GLN z 98 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 85446 Z= 0.239 Angle : 0.641 10.605 124992 Z= 0.326 Chirality : 0.038 0.295 15658 Planarity : 0.005 0.062 8644 Dihedral : 16.889 179.683 28946 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.11 % Favored : 94.75 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.12), residues: 4886 helix: 0.61 (0.12), residues: 1881 sheet: -0.66 (0.20), residues: 618 loop : -0.94 (0.13), residues: 2387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 646 time to evaluate : 5.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 52 residues processed: 685 average time/residue: 0.7759 time to fit residues: 908.5662 Evaluate side-chains 636 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 584 time to evaluate : 4.558 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.5893 time to fit residues: 64.3877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 341 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 chunk 511 optimal weight: 10.0000 chunk 418 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 615 optimal weight: 2.9990 chunk 665 optimal weight: 9.9990 chunk 548 optimal weight: 8.9990 chunk 610 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 494 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN E 75 GLN F 69 GLN H 77 ASN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 GLN b 55 GLN ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN r 3 GLN r 40 GLN ** y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 85446 Z= 0.248 Angle : 0.611 11.378 124992 Z= 0.312 Chirality : 0.038 0.288 15658 Planarity : 0.005 0.067 8644 Dihedral : 16.785 179.899 28946 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.19 % Favored : 94.69 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.12), residues: 4886 helix: 0.79 (0.12), residues: 1879 sheet: -0.70 (0.20), residues: 631 loop : -0.90 (0.13), residues: 2376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 627 time to evaluate : 4.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 25 residues processed: 657 average time/residue: 0.7707 time to fit residues: 869.3931 Evaluate side-chains 595 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 570 time to evaluate : 4.457 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.5967 time to fit residues: 33.7684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 608 optimal weight: 7.9990 chunk 463 optimal weight: 8.9990 chunk 319 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 293 optimal weight: 0.0170 chunk 413 optimal weight: 0.9980 chunk 618 optimal weight: 50.0000 chunk 654 optimal weight: 4.9990 chunk 322 optimal weight: 3.9990 chunk 585 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN E 75 GLN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 GLN N 123 GLN ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN b 55 GLN ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 406 ASN h 13 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN ** y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN z 98 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 85446 Z= 0.287 Angle : 0.627 9.822 124992 Z= 0.319 Chirality : 0.038 0.293 15658 Planarity : 0.005 0.070 8644 Dihedral : 16.747 179.730 28946 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.43 % Favored : 94.44 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.12), residues: 4886 helix: 0.88 (0.12), residues: 1872 sheet: -0.60 (0.20), residues: 620 loop : -0.89 (0.13), residues: 2394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 609 time to evaluate : 4.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 56 residues processed: 660 average time/residue: 0.7806 time to fit residues: 878.9847 Evaluate side-chains 617 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 561 time to evaluate : 4.472 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.6104 time to fit residues: 70.5225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 545 optimal weight: 20.0000 chunk 371 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 487 optimal weight: 50.0000 chunk 270 optimal weight: 0.6980 chunk 558 optimal weight: 2.9990 chunk 452 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 334 optimal weight: 6.9990 chunk 587 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 ASN M 85 ASN N 123 GLN ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 27 GLN ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 406 ASN ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN ** y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN y 162 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 85446 Z= 0.389 Angle : 0.700 10.263 124992 Z= 0.355 Chirality : 0.042 0.303 15658 Planarity : 0.005 0.071 8644 Dihedral : 16.889 179.858 28946 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.11 % Favored : 93.77 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.12), residues: 4886 helix: 0.74 (0.12), residues: 1876 sheet: -0.59 (0.21), residues: 615 loop : -0.98 (0.13), residues: 2395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 599 time to evaluate : 4.548 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 outliers start: 104 outliers final: 58 residues processed: 672 average time/residue: 0.7856 time to fit residues: 904.6108 Evaluate side-chains 622 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 564 time to evaluate : 4.472 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.6012 time to fit residues: 71.5546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 220 optimal weight: 0.9980 chunk 589 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 384 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 chunk 655 optimal weight: 0.7980 chunk 543 optimal weight: 5.9990 chunk 303 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 343 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN A L 146 GLN ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 GLN Q 78 GLN ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 13 GLN ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN ** y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN z 98 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 85446 Z= 0.183 Angle : 0.592 11.511 124992 Z= 0.302 Chirality : 0.036 0.371 15658 Planarity : 0.004 0.067 8644 Dihedral : 16.679 179.979 28946 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.74 % Favored : 95.10 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.12), residues: 4886 helix: 0.93 (0.12), residues: 1880 sheet: -0.58 (0.20), residues: 628 loop : -0.81 (0.13), residues: 2378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 627 time to evaluate : 4.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 33 residues processed: 659 average time/residue: 0.7838 time to fit residues: 882.5229 Evaluate side-chains 603 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 570 time to evaluate : 4.393 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5926 time to fit residues: 42.5012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 631 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 373 optimal weight: 6.9990 chunk 478 optimal weight: 40.0000 chunk 370 optimal weight: 0.9990 chunk 551 optimal weight: 2.9990 chunk 365 optimal weight: 3.9990 chunk 652 optimal weight: 0.9980 chunk 408 optimal weight: 0.0020 chunk 397 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 55 GLN ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 406 ASN ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN ** y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN y 162 HIS ** y 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 85446 Z= 0.175 Angle : 0.576 9.447 124992 Z= 0.294 Chirality : 0.036 0.259 15658 Planarity : 0.004 0.063 8644 Dihedral : 16.501 179.789 28946 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.92 % Favored : 94.94 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.12), residues: 4886 helix: 1.02 (0.12), residues: 1876 sheet: -0.50 (0.20), residues: 626 loop : -0.74 (0.13), residues: 2384 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 620 time to evaluate : 4.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 28 residues processed: 640 average time/residue: 0.8174 time to fit residues: 898.3190 Evaluate side-chains 601 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 573 time to evaluate : 4.578 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.6137 time to fit residues: 38.6829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 403 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 389 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 414 optimal weight: 4.9990 chunk 444 optimal weight: 0.7980 chunk 322 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 512 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 GLN O 51 ASN Q 78 GLN ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN ** y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN ** y 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 85446 Z= 0.305 Angle : 0.634 12.430 124992 Z= 0.322 Chirality : 0.038 0.275 15658 Planarity : 0.005 0.066 8644 Dihedral : 16.560 179.976 28946 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.50 % Favored : 94.40 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.12), residues: 4886 helix: 0.94 (0.12), residues: 1876 sheet: -0.52 (0.20), residues: 621 loop : -0.78 (0.13), residues: 2389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 583 time to evaluate : 6.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 25 residues processed: 604 average time/residue: 0.7979 time to fit residues: 822.3475 Evaluate side-chains 587 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 562 time to evaluate : 4.471 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.6046 time to fit residues: 33.9703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 593 optimal weight: 0.7980 chunk 625 optimal weight: 50.0000 chunk 570 optimal weight: 0.7980 chunk 608 optimal weight: 0.6980 chunk 624 optimal weight: 0.5980 chunk 365 optimal weight: 3.9990 chunk 264 optimal weight: 0.7980 chunk 477 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 549 optimal weight: 0.0770 chunk 575 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN A ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 GLN ** S 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 GLN ** a 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 13 GLN ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 HIS ** y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN y 168 GLN z 98 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 85446 Z= 0.145 Angle : 0.573 10.390 124992 Z= 0.293 Chirality : 0.035 0.257 15658 Planarity : 0.004 0.060 8644 Dihedral : 16.371 179.754 28946 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.41 % Favored : 95.49 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.12), residues: 4886 helix: 0.99 (0.12), residues: 1897 sheet: -0.38 (0.21), residues: 620 loop : -0.69 (0.13), residues: 2369 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 616 time to evaluate : 4.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 626 average time/residue: 0.7868 time to fit residues: 842.6976 Evaluate side-chains 574 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 561 time to evaluate : 4.455 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5942 time to fit residues: 20.0695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 605 optimal weight: 10.0000 chunk 399 optimal weight: 0.8980 chunk 642 optimal weight: 9.9990 chunk 392 optimal weight: 0.9990 chunk 305 optimal weight: 1.9990 chunk 446 optimal weight: 0.9990 chunk 674 optimal weight: 4.9990 chunk 620 optimal weight: 50.0000 chunk 537 optimal weight: 40.0000 chunk 55 optimal weight: 5.9990 chunk 414 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN G 182 ASN A N 32 GLN ** S 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 46 GLN ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 HIS ** y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN ** y 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 85446 Z= 0.243 Angle : 0.600 10.090 124992 Z= 0.306 Chirality : 0.037 0.352 15658 Planarity : 0.004 0.065 8644 Dihedral : 16.344 179.742 28946 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.71 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.12), residues: 4886 helix: 1.04 (0.12), residues: 1881 sheet: -0.38 (0.20), residues: 614 loop : -0.68 (0.13), residues: 2391 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 569 time to evaluate : 4.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 577 average time/residue: 0.7952 time to fit residues: 784.9074 Evaluate side-chains 569 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 556 time to evaluate : 4.483 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.6156 time to fit residues: 20.3356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 329 optimal weight: 4.9990 chunk 426 optimal weight: 0.7980 chunk 572 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 495 optimal weight: 0.0980 chunk 79 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 537 optimal weight: 40.0000 chunk 225 optimal weight: 0.8980 chunk 552 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 GLN ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 46 GLN h 15 ASN h 19 GLN ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN ** y 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 98 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.113238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.089010 restraints weight = 252368.233| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.36 r_work: 0.3055 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 85446 Z= 0.302 Angle : 0.643 10.711 124992 Z= 0.328 Chirality : 0.039 0.351 15658 Planarity : 0.005 0.064 8644 Dihedral : 16.455 179.567 28946 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.70 % Favored : 94.20 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.12), residues: 4886 helix: 0.89 (0.12), residues: 1883 sheet: -0.54 (0.20), residues: 627 loop : -0.78 (0.13), residues: 2376 =============================================================================== Job complete usr+sys time: 16005.22 seconds wall clock time: 286 minutes 9.80 seconds (17169.80 seconds total)