Starting phenix.real_space_refine (version: dev) on Fri Feb 24 20:03:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmf_10519/02_2023/6tmf_10519_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmf_10519/02_2023/6tmf_10519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmf_10519/02_2023/6tmf_10519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmf_10519/02_2023/6tmf_10519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmf_10519/02_2023/6tmf_10519_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmf_10519/02_2023/6tmf_10519_updated.pdb" } resolution = 2.8 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= 0.004 sd= 1.121 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "B ASP 9": "OD1" <-> "OD2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 97": "NH1" <-> "NH2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "E ASP 24": "OD1" <-> "OD2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 8": "NH1" <-> "NH2" Residue "F ASP 17": "OD1" <-> "OD2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 25": "NH1" <-> "NH2" Residue "F TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F ASP 180": "OD1" <-> "OD2" Residue "F ARG 189": "NH1" <-> "NH2" Residue "F PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G ASP 60": "OD1" <-> "OD2" Residue "G ASP 69": "OD1" <-> "OD2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 12": "NH1" <-> "NH2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 90": "NH1" <-> "NH2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H GLU 101": "OE1" <-> "OE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I GLU 40": "OE1" <-> "OE2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J GLU 85": "OE1" <-> "OE2" Residue "J GLU 90": "OE1" <-> "OE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 92": "NH1" <-> "NH2" Residue "K ASP 93": "OD1" <-> "OD2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "L ARG 25": "NH1" <-> "NH2" Residue "L ARG 27": "NH1" <-> "NH2" Residue "L GLU 34": "OE1" <-> "OE2" Residue "L ASP 63": "OD1" <-> "OD2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 110": "OD1" <-> "OD2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M ARG 29": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M GLU 65": "OE1" <-> "OE2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N ASP 55": "OD1" <-> "OD2" Residue "N GLU 56": "OE1" <-> "OE2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N ARG 113": "NH1" <-> "NH2" Residue "N ASP 119": "OD1" <-> "OD2" Residue "N ARG 135": "NH1" <-> "NH2" Residue "O GLU 39": "OE1" <-> "OE2" Residue "O GLU 45": "OE1" <-> "OE2" Residue "O GLU 56": "OE1" <-> "OE2" Residue "O ASP 98": "OD1" <-> "OD2" Residue "O ARG 141": "NH1" <-> "NH2" Residue "O GLU 143": "OE1" <-> "OE2" Residue "P ASP 3": "OD1" <-> "OD2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "P TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 87": "OE1" <-> "OE2" Residue "P ASP 91": "OD1" <-> "OD2" Residue "P TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 122": "OE1" <-> "OE2" Residue "P ARG 133": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 40": "NH1" <-> "NH2" Residue "Q PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 9": "NH1" <-> "NH2" Residue "R GLU 27": "OE1" <-> "OE2" Residue "S PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 40": "OD1" <-> "OD2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "S GLU 60": "OE1" <-> "OE2" Residue "S TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 78": "OD1" <-> "OD2" Residue "T ARG 14": "NH1" <-> "NH2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T GLU 37": "OE1" <-> "OE2" Residue "T GLU 63": "OE1" <-> "OE2" Residue "U ARG 32": "NH1" <-> "NH2" Residue "U ARG 56": "NH1" <-> "NH2" Residue "U PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 106": "OE1" <-> "OE2" Residue "U ARG 111": "NH1" <-> "NH2" Residue "V GLU 24": "OE1" <-> "OE2" Residue "V GLU 42": "OE1" <-> "OE2" Residue "V ARG 43": "NH1" <-> "NH2" Residue "V GLU 46": "OE1" <-> "OE2" Residue "V TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 65": "OD1" <-> "OD2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "X PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 22": "OD1" <-> "OD2" Residue "X ARG 33": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X GLU 76": "OE1" <-> "OE2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 16": "NH1" <-> "NH2" Residue "a ASP 52": "OD1" <-> "OD2" Residue "a GLU 60": "OE1" <-> "OE2" Residue "a GLU 62": "OE1" <-> "OE2" Residue "b GLU 61": "OE1" <-> "OE2" Residue "b TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 85": "OE1" <-> "OE2" Residue "b GLU 112": "OE1" <-> "OE2" Residue "b ASP 113": "OD1" <-> "OD2" Residue "d ARG 28": "NH1" <-> "NH2" Residue "d TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 129": "OD1" <-> "OD2" Residue "d ARG 144": "NH1" <-> "NH2" Residue "d TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 194": "OD1" <-> "OD2" Residue "d GLU 195": "OE1" <-> "OE2" Residue "d ARG 293": "NH1" <-> "NH2" Residue "d ARG 301": "NH1" <-> "NH2" Residue "d GLU 315": "OE1" <-> "OE2" Residue "d GLU 323": "OE1" <-> "OE2" Residue "d ASP 355": "OD1" <-> "OD2" Residue "d GLU 367": "OE1" <-> "OE2" Residue "d GLU 426": "OE1" <-> "OE2" Residue "d PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 454": "OE1" <-> "OE2" Residue "d GLU 477": "OE1" <-> "OE2" Residue "d ASP 519": "OD1" <-> "OD2" Residue "d ASP 524": "OD1" <-> "OD2" Residue "d ARG 565": "NH1" <-> "NH2" Residue "d ASP 567": "OD1" <-> "OD2" Residue "d ARG 584": "NH1" <-> "NH2" Residue "d GLU 588": "OE1" <-> "OE2" Residue "d ARG 589": "NH1" <-> "NH2" Residue "d ASP 591": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 65449 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 31920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1485, 31920 Classifications: {'RNA': 1485} Modifications used: {'rna2p_pur': 113, 'rna2p_pyr': 80, 'rna3p_pur': 724, 'rna3p_pyr': 568} Link IDs: {'rna2p': 192, 'rna3p': 1292} Chain: "B" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1571 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "C" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1526 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain: "D" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1520 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain: "E" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1476 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 169} Chain: "F" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1963 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "G" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1721 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 8, 'TRANS': 211} Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 116} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1704 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "J" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1022 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1040 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "M" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 819 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "N" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1005 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "O" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1131 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain: "P" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1109 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "Q" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 459 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "R" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1225 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 140} Chain: "S" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 913 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "T" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 540 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "U" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 949 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "V" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1218 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 10, 'TRANS': 138} Chain: "W" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 435 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 6, 'TRANS': 49} Chain: "X" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "Y" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 475 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "Z" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 417 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "a" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 514 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 936 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 113} Chain: "c" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 351 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "d" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4622 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 561} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Unusual residues: {' MG': 27} Classifications: {'undetermined': 27} Link IDs: {None: 26} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {' MG': 2, 'ANP': 2, 'SF4': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 51657 SG CYS Q 21 66.016 80.359 167.613 1.00 15.56 S ATOM 51681 SG CYS Q 24 68.182 81.194 164.493 1.00 16.72 S ATOM 51794 SG CYS Q 39 67.682 84.251 166.328 1.00 14.61 S ATOM 51821 SG CYS Q 42 64.221 83.210 164.830 1.00 14.58 S ATOM 56984 SG CYS W 28 21.118 149.447 123.456 1.00 21.12 S ATOM 57005 SG CYS W 31 17.177 149.557 121.586 1.00 26.33 S ATOM 57164 SG CYS W 51 20.970 148.871 119.979 1.00 20.62 S ATOM 57186 SG CYS W 54 20.119 151.508 121.372 1.00 24.40 S ATOM 56845 SG CYS W 10 32.289 142.348 117.986 1.00 15.94 S ATOM 56864 SG CYS W 13 34.487 141.687 115.183 1.00 18.75 S ATOM 57070 SG CYS W 39 35.746 140.931 118.147 1.00 14.20 S ATOM 57091 SG CYS W 42 35.786 144.290 118.135 1.00 13.59 S ATOM 58171 SG CYS Y 20 51.623 203.188 111.393 1.00 28.53 S ATOM 58314 SG CYS Y 39 53.806 201.441 108.740 1.00 25.44 S ATOM 58335 SG CYS Y 42 55.653 203.728 110.361 1.00 26.40 S ATOM 60910 SG CYS d 24 104.529 92.014 93.381 1.00 14.47 S ATOM 61113 SG CYS d 51 102.994 87.629 87.553 1.00 13.27 S ATOM 61149 SG CYS d 57 104.165 93.972 86.257 1.00 12.11 S ATOM 61131 SG CYS d 54 98.987 92.317 90.098 1.00 11.12 S ATOM 61180 SG CYS d 61 108.301 99.729 82.994 1.00 15.15 S ATOM 60807 SG CYS d 11 114.710 96.960 82.905 1.00 21.30 S Time building chain proxies: 27.36, per 1000 atoms: 0.42 Number of scatterers: 65449 At special positions: 0 Unit cell: (145.256, 214.632, 247.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Fe 8 26.01 S 136 16.00 P 1491 15.00 Mg 29 11.99 O 16256 8.00 N 12110 7.00 C 35415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.94 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 d 601 " pdb="FE2 SF4 d 601 " - pdb=" SG CYS d 51 " pdb="FE4 SF4 d 601 " - pdb=" SG CYS d 54 " pdb="FE1 SF4 d 601 " - pdb=" SG CYS d 24 " pdb="FE3 SF4 d 601 " - pdb=" SG CYS d 57 " pdb=" SF4 d 602 " pdb="FE3 SF4 d 602 " - pdb=" SG CYS d 61 " pdb="FE4 SF4 d 602 " - pdb=" SG CYS d 11 " pdb="FE2 SF4 d 602 " - pdb=" SG CYS d 16 " pdb="FE1 SF4 d 602 " - pdb=" SG CYS d 20 " Number of angles added : 24 Zn2+ tetrahedral coordination pdb=" ZN Q 101 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 39 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 24 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 21 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 42 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 54 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 51 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 28 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 31 " pdb=" ZN W 102 " pdb="ZN ZN W 102 " - pdb=" SG CYS W 13 " pdb="ZN ZN W 102 " - pdb=" SG CYS W 10 " pdb="ZN ZN W 102 " - pdb=" SG CYS W 42 " pdb="ZN ZN W 102 " - pdb=" SG CYS W 39 " pdb=" ZN Y 101 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 42 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 20 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 39 " Number of angles added : 18 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7684 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 43 sheets defined 31.9% alpha, 15.7% beta 521 base pairs and 833 stacking pairs defined. Time for finding SS restraints: 22.05 Creating SS restraints... Processing helix chain 'B' and resid 9 through 14 Processing helix chain 'B' and resid 44 through 60 Processing helix chain 'B' and resid 73 through 86 Proline residue: B 78 - end of helix Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 160 through 178 removed outlier: 6.110A pdb=" N LEU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 191 through 194 No H-bonds generated for 'chain 'B' and resid 191 through 194' Processing helix chain 'C' and resid 3 through 24 Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 51 through 55 Processing helix chain 'C' and resid 60 through 72 Processing helix chain 'C' and resid 93 through 105 Processing helix chain 'C' and resid 109 through 123 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' Processing helix chain 'D' and resid 44 through 47 Processing helix chain 'D' and resid 93 through 99 Processing helix chain 'D' and resid 135 through 155 Processing helix chain 'D' and resid 158 through 166 Processing helix chain 'D' and resid 169 through 175 Processing helix chain 'E' and resid 20 through 33 Processing helix chain 'E' and resid 38 through 59 Processing helix chain 'E' and resid 68 through 80 Processing helix chain 'E' and resid 89 through 94 Processing helix chain 'E' and resid 97 through 103 Processing helix chain 'E' and resid 105 through 110 Processing helix chain 'E' and resid 118 through 127 Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 159 through 161 No H-bonds generated for 'chain 'E' and resid 159 through 161' Processing helix chain 'E' and resid 166 through 173 Processing helix chain 'F' and resid 12 through 14 No H-bonds generated for 'chain 'F' and resid 12 through 14' Processing helix chain 'F' and resid 39 through 41 No H-bonds generated for 'chain 'F' and resid 39 through 41' Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 59 through 68 Processing helix chain 'F' and resid 117 through 121 Processing helix chain 'G' and resid 3 through 8 removed outlier: 3.895A pdb=" N GLU G 8 " --> pdb=" O ARG G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 20 Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 40 through 46 Processing helix chain 'G' and resid 48 through 51 Processing helix chain 'G' and resid 99 through 112 Processing helix chain 'G' and resid 162 through 171 Processing helix chain 'G' and resid 187 through 203 removed outlier: 4.373A pdb=" N ASN G 202 " --> pdb=" O LEU G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 214 removed outlier: 3.582A pdb=" N GLU G 211 " --> pdb=" O PRO G 208 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR G 214 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 40 through 43 No H-bonds generated for 'chain 'H' and resid 40 through 43' Processing helix chain 'I' and resid 17 through 19 No H-bonds generated for 'chain 'I' and resid 17 through 19' Processing helix chain 'I' and resid 31 through 36 Proline residue: I 35 - end of helix No H-bonds generated for 'chain 'I' and resid 31 through 36' Processing helix chain 'I' and resid 63 through 71 Processing helix chain 'I' and resid 81 through 83 No H-bonds generated for 'chain 'I' and resid 81 through 83' Processing helix chain 'I' and resid 97 through 113 Processing helix chain 'I' and resid 119 through 128 Processing helix chain 'I' and resid 154 through 173 Processing helix chain 'I' and resid 180 through 193 Processing helix chain 'I' and resid 199 through 214 Processing helix chain 'J' and resid 6 through 19 Processing helix chain 'J' and resid 32 through 43 Processing helix chain 'J' and resid 86 through 93 Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'K' and resid 25 through 27 No H-bonds generated for 'chain 'K' and resid 25 through 27' Processing helix chain 'K' and resid 87 through 92 Processing helix chain 'K' and resid 114 through 117 No H-bonds generated for 'chain 'K' and resid 114 through 117' Processing helix chain 'L' and resid 33 through 35 No H-bonds generated for 'chain 'L' and resid 33 through 35' Processing helix chain 'L' and resid 39 through 52 Proline residue: L 48 - end of helix Processing helix chain 'L' and resid 54 through 59 removed outlier: 4.849A pdb=" N GLY L 59 " --> pdb=" O GLU L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 90 Processing helix chain 'L' and resid 93 through 102 Processing helix chain 'L' and resid 104 through 106 No H-bonds generated for 'chain 'L' and resid 104 through 106' Processing helix chain 'M' and resid 13 through 29 Processing helix chain 'M' and resid 79 through 87 Processing helix chain 'N' and resid 46 through 49 No H-bonds generated for 'chain 'N' and resid 46 through 49' Processing helix chain 'N' and resid 53 through 56 No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'N' and resid 59 through 75 removed outlier: 6.339A pdb=" N ILE N 64 " --> pdb=" O TYR N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 110 Processing helix chain 'O' and resid 13 through 26 removed outlier: 3.972A pdb=" N SER O 26 " --> pdb=" O LYS O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 35 Processing helix chain 'O' and resid 37 through 41 Processing helix chain 'O' and resid 93 through 96 No H-bonds generated for 'chain 'O' and resid 93 through 96' Processing helix chain 'O' and resid 134 through 138 Processing helix chain 'P' and resid 22 through 28 Processing helix chain 'P' and resid 34 through 44 Processing helix chain 'P' and resid 52 through 54 No H-bonds generated for 'chain 'P' and resid 52 through 54' Processing helix chain 'P' and resid 57 through 68 Processing helix chain 'P' and resid 71 through 73 No H-bonds generated for 'chain 'P' and resid 71 through 73' Processing helix chain 'P' and resid 96 through 113 Processing helix chain 'P' and resid 116 through 123 Processing helix chain 'Q' and resid 40 through 50 Proline residue: Q 48 - end of helix Processing helix chain 'R' and resid 30 through 43 Processing helix chain 'R' and resid 47 through 56 Processing helix chain 'R' and resid 63 through 67 Processing helix chain 'R' and resid 71 through 77 Processing helix chain 'R' and resid 86 through 104 Processing helix chain 'R' and resid 109 through 132 Processing helix chain 'R' and resid 143 through 150 Processing helix chain 'T' and resid 7 through 19 Processing helix chain 'T' and resid 21 through 23 No H-bonds generated for 'chain 'T' and resid 21 through 23' Processing helix chain 'T' and resid 28 through 37 Processing helix chain 'T' and resid 44 through 63 Processing helix chain 'U' and resid 14 through 19 Processing helix chain 'U' and resid 22 through 28 Processing helix chain 'U' and resid 31 through 39 Processing helix chain 'U' and resid 43 through 56 Processing helix chain 'U' and resid 97 through 99 No H-bonds generated for 'chain 'U' and resid 97 through 99' Processing helix chain 'U' and resid 104 through 106 No H-bonds generated for 'chain 'U' and resid 104 through 106' Processing helix chain 'V' and resid 10 through 22 removed outlier: 4.359A pdb=" N GLU V 22 " --> pdb=" O LYS V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 50 through 64 Processing helix chain 'V' and resid 70 through 77 Processing helix chain 'V' and resid 96 through 108 Processing helix chain 'V' and resid 123 through 141 Processing helix chain 'V' and resid 145 through 148 No H-bonds generated for 'chain 'V' and resid 145 through 148' Processing helix chain 'W' and resid 40 through 44 Processing helix chain 'X' and resid 33 through 43 Processing helix chain 'X' and resid 75 through 81 Processing helix chain 'X' and resid 84 through 90 Processing helix chain 'b' and resid 13 through 27 removed outlier: 3.504A pdb=" N GLU b 17 " --> pdb=" O ALA b 13 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU b 25 " --> pdb=" O GLU b 21 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA b 26 " --> pdb=" O ALA b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 45 Processing helix chain 'b' and resid 63 through 66 No H-bonds generated for 'chain 'b' and resid 63 through 66' Processing helix chain 'b' and resid 70 through 72 No H-bonds generated for 'chain 'b' and resid 70 through 72' Processing helix chain 'b' and resid 83 through 89 Processing helix chain 'b' and resid 108 through 121 removed outlier: 4.256A pdb=" N ASP b 113 " --> pdb=" O GLU b 109 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 8 No H-bonds generated for 'chain 'c' and resid 5 through 8' Processing helix chain 'c' and resid 16 through 35 Processing helix chain 'd' and resid 19 through 22 No H-bonds generated for 'chain 'd' and resid 19 through 22' Processing helix chain 'd' and resid 25 through 29 Processing helix chain 'd' and resid 56 through 60 Processing helix chain 'd' and resid 112 through 120 Processing helix chain 'd' and resid 137 through 143 Processing helix chain 'd' and resid 148 through 156 Processing helix chain 'd' and resid 169 through 175 removed outlier: 4.443A pdb=" N PHE d 175 " --> pdb=" O TYR d 171 " (cutoff:3.500A) Processing helix chain 'd' and resid 180 through 187 Processing helix chain 'd' and resid 193 through 200 Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 215 through 228 Processing helix chain 'd' and resid 245 through 258 Processing helix chain 'd' and resid 271 through 275 Processing helix chain 'd' and resid 300 through 309 Processing helix chain 'd' and resid 382 through 389 Processing helix chain 'd' and resid 421 through 428 Processing helix chain 'd' and resid 438 through 442 Processing helix chain 'd' and resid 462 through 475 Processing helix chain 'd' and resid 492 through 509 Processing helix chain 'd' and resid 520 through 526 Processing helix chain 'd' and resid 549 through 558 Processing helix chain 'd' and resid 581 through 589 Processing sheet with id= A, first strand: chain 'B' and resid 137 through 140 removed outlier: 6.544A pdb=" N LEU B 151 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL B 140 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE B 153 " --> pdb=" O VAL B 140 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.878A pdb=" N VAL B 41 " --> pdb=" O TYR B 32 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 32 through 38 Processing sheet with id= D, first strand: chain 'C' and resid 142 through 149 Processing sheet with id= E, first strand: chain 'D' and resid 51 through 54 removed outlier: 6.090A pdb=" N GLN D 73 " --> pdb=" O PHE D 86 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N PHE D 86 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N LYS D 85 " --> pdb=" O ALA D 196 " (cutoff:3.500A) removed outlier: 11.769A pdb=" N ALA D 196 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LYS D 87 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS D 120 " --> pdb=" O LEU D 195 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 24 through 26 Processing sheet with id= G, first strand: chain 'E' and resid 130 through 132 Processing sheet with id= H, first strand: chain 'F' and resid 42 through 44 Processing sheet with id= I, first strand: chain 'F' and resid 89 through 93 Processing sheet with id= J, first strand: chain 'F' and resid 123 through 126 removed outlier: 4.754A pdb=" N GLU F 175 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS F 167 " --> pdb=" O VAL F 173 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL F 173 " --> pdb=" O LYS F 167 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 130 through 133 Processing sheet with id= L, first strand: chain 'F' and resid 230 through 234 removed outlier: 6.874A pdb=" N TYR F 184 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR F 214 " --> pdb=" O VAL F 200 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL F 202 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL F 212 " --> pdb=" O VAL F 202 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 88 through 96 removed outlier: 6.501A pdb=" N ALA G 81 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL G 58 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY G 83 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN G 56 " --> pdb=" O GLY G 83 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 138 through 142 Processing sheet with id= O, first strand: chain 'H' and resid 15 through 21 removed outlier: 3.699A pdb=" N GLY H 65 " --> pdb=" O ASN H 120 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LYS H 122 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE H 63 " --> pdb=" O LYS H 122 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL H 124 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU H 61 " --> pdb=" O VAL H 124 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 83 through 87 Processing sheet with id= Q, first strand: chain 'I' and resid 134 through 141 Processing sheet with id= R, first strand: chain 'J' and resid 24 through 27 Processing sheet with id= S, first strand: chain 'J' and resid 71 through 74 removed outlier: 6.846A pdb=" N ILE J 103 " --> pdb=" O ILE J 126 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR J 128 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE J 101 " --> pdb=" O TYR J 128 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 79 through 81 Processing sheet with id= U, first strand: chain 'K' and resid 71 through 73 Processing sheet with id= V, first strand: chain 'K' and resid 43 through 49 removed outlier: 6.575A pdb=" N LYS K 45 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU K 58 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE K 47 " --> pdb=" O VAL K 56 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL K 56 " --> pdb=" O ILE K 47 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR K 49 " --> pdb=" O ARG K 54 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ARG K 54 " --> pdb=" O THR K 49 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 3 through 9 Processing sheet with id= X, first strand: chain 'M' and resid 94 through 101 removed outlier: 4.609A pdb=" N LYS M 70 " --> pdb=" O LEU M 40 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 43 through 50 Processing sheet with id= Z, first strand: chain 'N' and resid 40 through 45 removed outlier: 6.520A pdb=" N ILE N 32 " --> pdb=" O VAL N 41 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG N 43 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE N 30 " --> pdb=" O ARG N 43 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER N 45 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR N 28 " --> pdb=" O SER N 45 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY N 80 " --> pdb=" O GLY N 17 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA N 19 " --> pdb=" O GLY N 80 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N HIS N 82 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE N 21 " --> pdb=" O HIS N 82 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS N 84 " --> pdb=" O ILE N 21 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N SER N 23 " --> pdb=" O LYS N 84 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG N 86 " --> pdb=" O SER N 23 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'O' and resid 82 through 87 removed outlier: 6.233A pdb=" N GLN O 76 " --> pdb=" O VAL O 54 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL O 54 " --> pdb=" O GLN O 76 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS O 128 " --> pdb=" O ILE O 104 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU O 106 " --> pdb=" O VAL O 126 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL O 126 " --> pdb=" O GLU O 106 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S' and resid 61 through 68 removed outlier: 3.744A pdb=" N SER S 39 " --> pdb=" O VAL S 47 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU S 49 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL S 37 " --> pdb=" O GLU S 49 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ARG S 51 " --> pdb=" O GLY S 35 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N GLY S 35 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 15.390A pdb=" N TYR S 53 " --> pdb=" O PHE S 33 " (cutoff:3.500A) removed outlier: 16.554A pdb=" N PHE S 33 " --> pdb=" O TYR S 53 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA S 103 " --> pdb=" O LEU S 86 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA S 88 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL S 101 " --> pdb=" O ALA S 88 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'U' and resid 64 through 66 removed outlier: 4.381A pdb=" N ILE U 64 " --> pdb=" O THR U 81 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'V' and resid 79 through 81 removed outlier: 3.935A pdb=" N HIS V 89 " --> pdb=" O LYS V 81 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'V' and resid 111 through 113 Processing sheet with id= AF, first strand: chain 'W' and resid 24 through 27 Processing sheet with id= AG, first strand: chain 'X' and resid 2 through 11 removed outlier: 6.786A pdb=" N TYR X 20 " --> pdb=" O ARG X 6 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET X 8 " --> pdb=" O GLU X 18 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU X 18 " --> pdb=" O MET X 8 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU X 10 " --> pdb=" O ARG X 16 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG X 16 " --> pdb=" O GLU X 10 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS X 70 " --> pdb=" O ILE X 53 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ILE X 53 " --> pdb=" O LYS X 70 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TYR X 72 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL X 51 " --> pdb=" O TYR X 72 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'Y' and resid 15 through 19 Processing sheet with id= AI, first strand: chain 'a' and resid 39 through 45 removed outlier: 3.512A pdb=" N GLU a 12 " --> pdb=" O LYS a 27 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG a 29 " --> pdb=" O VAL a 10 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL a 10 " --> pdb=" O ARG a 29 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'b' and resid 32 through 34 removed outlier: 3.886A pdb=" N ILE b 101 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU b 50 " --> pdb=" O ILE b 101 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE b 53 " --> pdb=" O PRO b 76 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE b 78 " --> pdb=" O ILE b 53 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'd' and resid 2 through 6 Processing sheet with id= AL, first strand: chain 'd' and resid 34 through 37 Processing sheet with id= AM, first strand: chain 'd' and resid 284 through 287 removed outlier: 6.813A pdb=" N LYS d 89 " --> pdb=" O GLY d 292 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL d 294 " --> pdb=" O LYS d 89 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N PHE d 91 " --> pdb=" O VAL d 294 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE d 88 " --> pdb=" O LYS d 84 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS d 84 " --> pdb=" O PHE d 88 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU d 90 " --> pdb=" O ARG d 82 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG d 82 " --> pdb=" O LEU d 90 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'd' and resid 280 through 282 removed outlier: 6.493A pdb=" N VAL d 264 " --> pdb=" O LEU d 102 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL d 104 " --> pdb=" O VAL d 264 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL d 266 " --> pdb=" O VAL d 104 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL d 163 " --> pdb=" O ILE d 235 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASP d 237 " --> pdb=" O VAL d 163 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS d 165 " --> pdb=" O ASP d 237 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'd' and resid 540 through 542 removed outlier: 8.243A pdb=" N GLY d 541 " --> pdb=" O ASP d 355 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN d 357 " --> pdb=" O GLY d 541 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN d 357 " --> pdb=" O LYS d 351 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS d 351 " --> pdb=" O GLN d 357 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'd' and resid 529 through 533 removed outlier: 6.186A pdb=" N THR d 513 " --> pdb=" O ILE d 371 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE d 373 " --> pdb=" O THR d 513 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE d 515 " --> pdb=" O ILE d 373 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N GLY d 375 " --> pdb=" O ILE d 515 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU d 483 " --> pdb=" O PHE d 514 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'd' and resid 564 through 566 1128 hydrogen bonds defined for protein. 3234 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1391 hydrogen bonds 2300 hydrogen bond angles 0 basepair planarities 521 basepair parallelities 833 stacking parallelities Total time for adding SS restraints: 41.70 Time building geometry restraints manager: 27.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.38: 26426 1.38 - 1.61: 42998 1.61 - 1.83: 368 1.83 - 2.05: 0 2.05 - 2.28: 24 Bond restraints: 69816 Sorted by residual: bond pdb=" C1' ANP d 603 " pdb=" C2' ANP d 603 " ideal model delta sigma weight residual 1.542 1.291 0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C1' ANP d 605 " pdb=" C2' ANP d 605 " ideal model delta sigma weight residual 1.542 1.296 0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C1' ANP d 605 " pdb=" O4' ANP d 605 " ideal model delta sigma weight residual 1.394 1.611 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C1' ANP d 603 " pdb=" O4' ANP d 603 " ideal model delta sigma weight residual 1.394 1.609 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C4' ANP d 603 " pdb=" O4' ANP d 603 " ideal model delta sigma weight residual 1.431 1.296 0.135 2.00e-02 2.50e+03 4.55e+01 ... (remaining 69811 not shown) Histogram of bond angle deviations from ideal: 73.18 - 86.99: 24 86.99 - 100.80: 204 100.80 - 114.61: 52788 114.61 - 128.43: 45690 128.43 - 142.24: 2879 Bond angle restraints: 101585 Sorted by residual: angle pdb=" N LYS O 5 " pdb=" CA LYS O 5 " pdb=" C LYS O 5 " ideal model delta sigma weight residual 110.10 122.13 -12.03 1.49e+00 4.50e-01 6.52e+01 angle pdb=" N GLY c 35 " pdb=" CA GLY c 35 " pdb=" C GLY c 35 " ideal model delta sigma weight residual 112.73 122.28 -9.55 1.20e+00 6.94e-01 6.33e+01 angle pdb=" N GLY E 63 " pdb=" CA GLY E 63 " pdb=" C GLY E 63 " ideal model delta sigma weight residual 113.18 130.04 -16.86 2.37e+00 1.78e-01 5.06e+01 angle pdb=" N ASP G 86 " pdb=" CA ASP G 86 " pdb=" C ASP G 86 " ideal model delta sigma weight residual 110.80 96.32 14.48 2.13e+00 2.20e-01 4.62e+01 angle pdb=" C ALA O 6 " pdb=" N PRO O 7 " pdb=" CA PRO O 7 " ideal model delta sigma weight residual 119.84 128.34 -8.50 1.25e+00 6.40e-01 4.62e+01 ... (remaining 101580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 37591 35.92 - 71.85: 1172 71.85 - 107.77: 90 107.77 - 143.70: 16 143.70 - 179.62: 29 Dihedral angle restraints: 38898 sinusoidal: 26926 harmonic: 11972 Sorted by residual: dihedral pdb=" O4' U A 158 " pdb=" C1' U A 158 " pdb=" N1 U A 158 " pdb=" C2 U A 158 " ideal model delta sinusoidal sigma weight residual 200.00 21.67 178.33 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A 422 " pdb=" C1' U A 422 " pdb=" N1 U A 422 " pdb=" C2 U A 422 " ideal model delta sinusoidal sigma weight residual 200.00 23.69 176.31 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U A 172 " pdb=" C1' U A 172 " pdb=" N1 U A 172 " pdb=" C2 U A 172 " ideal model delta sinusoidal sigma weight residual 200.00 32.30 167.70 1 1.50e+01 4.44e-03 8.44e+01 ... (remaining 38895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 11138 0.109 - 0.218: 1229 0.218 - 0.327: 59 0.327 - 0.436: 11 0.436 - 0.544: 1 Chirality restraints: 12438 Sorted by residual: chirality pdb=" CA LYS O 5 " pdb=" N LYS O 5 " pdb=" C LYS O 5 " pdb=" CB LYS O 5 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" CA ASN P 19 " pdb=" N ASN P 19 " pdb=" C ASN P 19 " pdb=" CB ASN P 19 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CA LYS d 136 " pdb=" N LYS d 136 " pdb=" C LYS d 136 " pdb=" CB LYS d 136 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 12435 not shown) Planarity restraints: 7352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 830 " 0.064 2.00e-02 2.50e+03 6.25e-02 8.78e+01 pdb=" N1 C A 830 " -0.042 2.00e-02 2.50e+03 pdb=" C2 C A 830 " -0.146 2.00e-02 2.50e+03 pdb=" O2 C A 830 " 0.066 2.00e-02 2.50e+03 pdb=" N3 C A 830 " 0.025 2.00e-02 2.50e+03 pdb=" C4 C A 830 " -0.024 2.00e-02 2.50e+03 pdb=" N4 C A 830 " 0.047 2.00e-02 2.50e+03 pdb=" C5 C A 830 " 0.008 2.00e-02 2.50e+03 pdb=" C6 C A 830 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 352 " 0.021 2.00e-02 2.50e+03 5.52e-02 6.84e+01 pdb=" N1 C A 352 " -0.008 2.00e-02 2.50e+03 pdb=" C2 C A 352 " -0.139 2.00e-02 2.50e+03 pdb=" O2 C A 352 " 0.076 2.00e-02 2.50e+03 pdb=" N3 C A 352 " 0.017 2.00e-02 2.50e+03 pdb=" C4 C A 352 " -0.021 2.00e-02 2.50e+03 pdb=" N4 C A 352 " 0.027 2.00e-02 2.50e+03 pdb=" C5 C A 352 " 0.012 2.00e-02 2.50e+03 pdb=" C6 C A 352 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A1000 " 0.009 2.00e-02 2.50e+03 5.11e-02 5.88e+01 pdb=" N1 C A1000 " -0.023 2.00e-02 2.50e+03 pdb=" C2 C A1000 " 0.124 2.00e-02 2.50e+03 pdb=" O2 C A1000 " -0.070 2.00e-02 2.50e+03 pdb=" N3 C A1000 " -0.026 2.00e-02 2.50e+03 pdb=" C4 C A1000 " 0.035 2.00e-02 2.50e+03 pdb=" N4 C A1000 " -0.017 2.00e-02 2.50e+03 pdb=" C5 C A1000 " -0.011 2.00e-02 2.50e+03 pdb=" C6 C A1000 " -0.022 2.00e-02 2.50e+03 ... (remaining 7349 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 249 2.38 - 3.01: 36119 3.01 - 3.64: 113812 3.64 - 4.27: 190755 4.27 - 4.90: 267573 Nonbonded interactions: 608508 Sorted by model distance: nonbonded pdb=" O2G ANP d 605 " pdb="MG MG d 606 " model vdw 1.750 2.170 nonbonded pdb=" OP2 G A1051 " pdb="MG MG A1520 " model vdw 1.797 2.170 nonbonded pdb=" O GLY d 53 " pdb=" S1 SF4 d 601 " model vdw 1.824 3.400 nonbonded pdb=" OP2 G A 94 " pdb="MG MG A1511 " model vdw 1.862 2.170 nonbonded pdb=" O GLU D 173 " pdb=" O LYS D 176 " model vdw 1.890 3.040 ... (remaining 608503 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 8 7.16 5 Zn 4 6.06 5 P 1491 5.49 5 Mg 29 5.21 5 S 136 5.16 5 C 35415 2.51 5 N 12110 2.21 5 O 16256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 12.950 Check model and map are aligned: 0.710 Process input model: 184.870 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.450 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 215.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.017 0.273 69816 Z= 1.050 Angle : 1.110 16.861 101585 Z= 0.563 Chirality : 0.071 0.544 12438 Planarity : 0.007 0.089 7352 Dihedral : 15.948 179.620 31214 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.51 % Favored : 89.98 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -3.66 (0.11), residues: 4112 helix: -2.13 (0.11), residues: 1460 sheet: -2.09 (0.17), residues: 763 loop : -2.74 (0.13), residues: 1889 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 917 time to evaluate : 3.789 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 outliers start: 26 outliers final: 14 residues processed: 938 average time/residue: 1.8503 time to fit residues: 2145.2107 Evaluate side-chains 656 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 642 time to evaluate : 3.746 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 1.1378 time to fit residues: 7.7260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 466 optimal weight: 3.9990 chunk 419 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 282 optimal weight: 0.9990 chunk 223 optimal weight: 0.8980 chunk 433 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 263 optimal weight: 0.9990 chunk 322 optimal weight: 1.9990 chunk 502 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN C 87 ASN C 123 ASN D 80 GLN D 81 ASN E 106 GLN E 135 GLN F 143 HIS F 148 HIS F 192 ASN G 56 GLN G 174 GLN H 18 GLN H 118 GLN I 29 ASN I 51 HIS ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN K 83 ASN K 88 GLN L 5 GLN L 117 HIS L 131 GLN M 84 GLN P 21 GLN R 57 GLN R 78 ASN T 30 HIS V 103 GLN Z 3 GLN ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 GLN d 70 ASN d 86 ASN d 126 ASN d 131 ASN d 167 GLN d 219 GLN d 282 HIS d 404 GLN ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 450 HIS d 456 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 69816 Z= 0.184 Angle : 0.647 13.343 101585 Z= 0.334 Chirality : 0.040 0.333 12438 Planarity : 0.005 0.056 7352 Dihedral : 14.680 179.661 22524 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.93 % Favored : 92.95 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.13), residues: 4112 helix: -0.10 (0.13), residues: 1413 sheet: -1.59 (0.18), residues: 737 loop : -1.91 (0.14), residues: 1962 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 774 time to evaluate : 4.107 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: 125 outliers final: 45 residues processed: 827 average time/residue: 1.6762 time to fit residues: 1754.5606 Evaluate side-chains 721 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 676 time to evaluate : 3.710 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 18 residues processed: 27 average time/residue: 0.6389 time to fit residues: 33.5754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 279 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 417 optimal weight: 4.9990 chunk 341 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 503 optimal weight: 0.6980 chunk 543 optimal weight: 1.9990 chunk 448 optimal weight: 1.9990 chunk 498 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 403 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 80 GLN E 75 GLN E 120 GLN F 192 ASN G 55 ASN G 113 ASN ** H 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN H 120 ASN I 182 GLN K 88 GLN L 131 GLN O 76 GLN P 17 ASN P 21 GLN R 57 GLN R 78 ASN U 45 GLN ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 GLN d 86 ASN d 131 ASN d 404 GLN ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 448 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 69816 Z= 0.300 Angle : 0.665 11.344 101585 Z= 0.344 Chirality : 0.042 0.356 12438 Planarity : 0.005 0.063 7352 Dihedral : 14.672 179.257 22524 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.49 % Favored : 92.39 % Rotamer Outliers : 4.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 4112 helix: 0.45 (0.14), residues: 1394 sheet: -1.28 (0.18), residues: 743 loop : -1.55 (0.14), residues: 1975 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 709 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 160 outliers final: 71 residues processed: 800 average time/residue: 1.6758 time to fit residues: 1698.6989 Evaluate side-chains 729 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 658 time to evaluate : 3.866 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 40 residues processed: 32 average time/residue: 0.7498 time to fit residues: 43.2450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 497 optimal weight: 0.4980 chunk 378 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 337 optimal weight: 10.0000 chunk 504 optimal weight: 6.9990 chunk 534 optimal weight: 20.0000 chunk 263 optimal weight: 2.9990 chunk 478 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN C 95 GLN E 37 ASN E 75 GLN E 120 GLN F 192 ASN G 113 ASN H 13 ASN H 18 GLN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN K 83 ASN K 88 GLN L 131 GLN P 21 GLN R 57 GLN R 78 ASN ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 GLN ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 69816 Z= 0.238 Angle : 0.620 10.873 101585 Z= 0.321 Chirality : 0.040 0.351 12438 Planarity : 0.005 0.056 7352 Dihedral : 14.622 178.984 22524 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.25 % Favored : 92.66 % Rotamer Outliers : 4.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.99 (0.13), residues: 4112 helix: 0.67 (0.14), residues: 1389 sheet: -1.09 (0.19), residues: 739 loop : -1.43 (0.14), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 700 time to evaluate : 3.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 95 residues processed: 794 average time/residue: 1.6496 time to fit residues: 1668.5598 Evaluate side-chains 762 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 667 time to evaluate : 4.789 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 57 residues processed: 40 average time/residue: 0.7776 time to fit residues: 54.3204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 445 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 397 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 456 optimal weight: 0.9980 chunk 369 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 479 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 37 ASN E 75 GLN F 192 ASN G 113 ASN H 18 GLN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN J 64 GLN K 88 GLN L 131 GLN O 49 GLN P 21 GLN R 57 GLN R 78 ASN ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 69816 Z= 0.346 Angle : 0.675 11.779 101585 Z= 0.349 Chirality : 0.043 0.367 12438 Planarity : 0.005 0.070 7352 Dihedral : 14.735 178.756 22524 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.64 % Favored : 92.27 % Rotamer Outliers : 5.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.92 (0.13), residues: 4112 helix: 0.67 (0.14), residues: 1379 sheet: -0.98 (0.19), residues: 726 loop : -1.37 (0.14), residues: 2007 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 698 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 199 outliers final: 103 residues processed: 812 average time/residue: 1.6085 time to fit residues: 1672.2365 Evaluate side-chains 767 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 664 time to evaluate : 3.795 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 61 residues processed: 43 average time/residue: 0.7143 time to fit residues: 54.4932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 179 optimal weight: 6.9990 chunk 481 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 313 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 535 optimal weight: 4.9990 chunk 444 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 280 optimal weight: 0.0470 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 75 GLN F 192 ASN G 113 ASN H 18 GLN I 182 GLN K 88 GLN L 131 GLN O 49 GLN P 21 GLN R 57 GLN R 78 ASN ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 211 ASN ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 69816 Z= 0.292 Angle : 0.647 11.666 101585 Z= 0.335 Chirality : 0.041 0.359 12438 Planarity : 0.005 0.061 7352 Dihedral : 14.717 178.621 22524 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.64 % Favored : 92.27 % Rotamer Outliers : 5.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.84 (0.13), residues: 4112 helix: 0.71 (0.14), residues: 1378 sheet: -0.96 (0.19), residues: 737 loop : -1.29 (0.14), residues: 1997 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 689 time to evaluate : 3.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 177 outliers final: 103 residues processed: 801 average time/residue: 1.6459 time to fit residues: 1683.7279 Evaluate side-chains 770 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 667 time to evaluate : 3.794 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 72 residues processed: 32 average time/residue: 0.7452 time to fit residues: 42.5471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 515 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 304 optimal weight: 0.8980 chunk 390 optimal weight: 0.7980 chunk 302 optimal weight: 3.9990 chunk 450 optimal weight: 0.0770 chunk 298 optimal weight: 5.9990 chunk 533 optimal weight: 7.9990 chunk 333 optimal weight: 3.9990 chunk 324 optimal weight: 6.9990 chunk 246 optimal weight: 0.8980 overall best weight: 1.3340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 81 ASN E 75 GLN F 192 ASN G 113 ASN ** H 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN I 29 ASN I 182 GLN J 42 GLN J 64 GLN K 88 GLN L 131 GLN O 49 GLN P 21 GLN R 57 GLN R 78 ASN ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 86 ASN ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 69816 Z= 0.196 Angle : 0.612 11.273 101585 Z= 0.316 Chirality : 0.039 0.342 12438 Planarity : 0.005 0.064 7352 Dihedral : 14.640 178.804 22524 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.39 % Favored : 92.51 % Rotamer Outliers : 4.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.74 (0.13), residues: 4112 helix: 0.84 (0.14), residues: 1384 sheet: -0.91 (0.19), residues: 723 loop : -1.26 (0.14), residues: 2005 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 693 time to evaluate : 4.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 153 outliers final: 94 residues processed: 798 average time/residue: 1.6134 time to fit residues: 1642.7001 Evaluate side-chains 758 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 664 time to evaluate : 3.762 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 74 residues processed: 22 average time/residue: 0.8332 time to fit residues: 32.6678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 329 optimal weight: 0.7980 chunk 212 optimal weight: 7.9990 chunk 318 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 338 optimal weight: 2.9990 chunk 363 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 418 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 81 ASN E 37 ASN E 75 GLN F 192 ASN G 113 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 GLN L 5 GLN L 131 GLN O 49 GLN P 21 GLN R 57 GLN R 78 ASN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 GLN ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 69816 Z= 0.231 Angle : 0.618 11.165 101585 Z= 0.319 Chirality : 0.039 0.350 12438 Planarity : 0.005 0.065 7352 Dihedral : 14.610 179.434 22524 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.30 % Favored : 92.61 % Rotamer Outliers : 3.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.70 (0.13), residues: 4112 helix: 0.86 (0.14), residues: 1390 sheet: -0.90 (0.19), residues: 737 loop : -1.24 (0.14), residues: 1985 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 671 time to evaluate : 4.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 92 residues processed: 761 average time/residue: 1.6566 time to fit residues: 1610.8284 Evaluate side-chains 741 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 649 time to evaluate : 3.747 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 73 residues processed: 21 average time/residue: 0.6502 time to fit residues: 27.6076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 484 optimal weight: 0.8980 chunk 510 optimal weight: 0.9980 chunk 465 optimal weight: 1.9990 chunk 496 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 390 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 448 optimal weight: 0.8980 chunk 469 optimal weight: 30.0000 chunk 494 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 81 ASN ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN F 192 ASN G 113 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN K 88 GLN ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 131 GLN O 49 GLN P 21 GLN R 57 GLN R 78 ASN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 GLN ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 69816 Z= 0.188 Angle : 0.610 10.644 101585 Z= 0.315 Chirality : 0.039 0.341 12438 Planarity : 0.005 0.073 7352 Dihedral : 14.605 179.328 22524 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.49 % Favored : 92.39 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.65 (0.13), residues: 4112 helix: 0.90 (0.14), residues: 1389 sheet: -0.83 (0.19), residues: 731 loop : -1.22 (0.14), residues: 1992 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 672 time to evaluate : 3.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 95 residues processed: 756 average time/residue: 1.6361 time to fit residues: 1581.3220 Evaluate side-chains 752 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 657 time to evaluate : 3.793 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 78 residues processed: 20 average time/residue: 0.6220 time to fit residues: 26.3258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 326 optimal weight: 6.9990 chunk 525 optimal weight: 4.9990 chunk 320 optimal weight: 0.7980 chunk 249 optimal weight: 0.9990 chunk 365 optimal weight: 1.9990 chunk 550 optimal weight: 6.9990 chunk 507 optimal weight: 0.6980 chunk 438 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 338 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 81 ASN ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN F 192 ASN G 113 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 GLN L 5 GLN L 131 GLN O 49 GLN P 21 GLN R 57 GLN R 78 ASN ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 69816 Z= 0.180 Angle : 0.609 14.230 101585 Z= 0.313 Chirality : 0.038 0.337 12438 Planarity : 0.005 0.069 7352 Dihedral : 14.570 179.606 22524 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.34 % Favored : 92.53 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.63 (0.13), residues: 4112 helix: 0.96 (0.14), residues: 1380 sheet: -0.84 (0.19), residues: 729 loop : -1.22 (0.14), residues: 2003 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 669 time to evaluate : 4.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 78 residues processed: 752 average time/residue: 1.6433 time to fit residues: 1578.2288 Evaluate side-chains 730 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 652 time to evaluate : 3.782 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 74 residues processed: 8 average time/residue: 0.7079 time to fit residues: 13.8424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 348 optimal weight: 9.9990 chunk 467 optimal weight: 0.4980 chunk 134 optimal weight: 6.9990 chunk 404 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 439 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 451 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 81 ASN E 75 GLN F 192 ASN G 113 ASN H 18 GLN J 64 GLN K 88 GLN L 5 GLN L 131 GLN O 49 GLN P 21 GLN R 57 GLN ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106319 restraints weight = 89786.020| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.09 r_work: 0.2823 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 69816 Z= 0.296 Angle : 0.652 13.361 101585 Z= 0.336 Chirality : 0.041 0.354 12438 Planarity : 0.005 0.066 7352 Dihedral : 14.627 179.552 22524 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.49 % Favored : 92.39 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.65 (0.13), residues: 4112 helix: 0.89 (0.14), residues: 1379 sheet: -0.82 (0.19), residues: 715 loop : -1.20 (0.14), residues: 2018 =============================================================================== Job complete usr+sys time: 21831.25 seconds wall clock time: 380 minutes 27.09 seconds (22827.09 seconds total)