Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 14:11:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/04_2023/5mps_3539_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/04_2023/5mps_3539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/04_2023/5mps_3539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/04_2023/5mps_3539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/04_2023/5mps_3539_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mps_3539/04_2023/5mps_3539_updated.pdb" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 2 8.98 5 Zn 6 6.06 5 P 348 5.49 5 Mg 3 5.21 5 S 192 5.16 5 C 36219 2.51 5 N 10406 2.21 5 O 11753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 1163": "NH1" <-> "NH2" Residue "A ARG 1442": "NH1" <-> "NH2" Residue "A PHE 1606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1650": "NH1" <-> "NH2" Residue "A ARG 1962": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 430": "NH1" <-> "NH2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 938": "NH1" <-> "NH2" Residue "H PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 349": "NH1" <-> "NH2" Residue "H ARG 382": "NH1" <-> "NH2" Residue "H ARG 439": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J ARG 186": "NH1" <-> "NH2" Residue "J TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K ARG 184": "NH1" <-> "NH2" Residue "K ARG 185": "NH1" <-> "NH2" Residue "K ARG 220": "NH1" <-> "NH2" Residue "L ARG 3": "NH1" <-> "NH2" Residue "L ARG 7": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 121": "NH1" <-> "NH2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "M ARG 161": "NH1" <-> "NH2" Residue "M ARG 166": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N ARG 111": "NH1" <-> "NH2" Residue "N ARG 252": "NH1" <-> "NH2" Residue "N ARG 261": "NH1" <-> "NH2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ARG 158": "NH1" <-> "NH2" Residue "O ARG 169": "NH1" <-> "NH2" Residue "O ARG 189": "NH1" <-> "NH2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "R ARG 22": "NH1" <-> "NH2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "S ARG 82": "NH1" <-> "NH2" Residue "S ARG 219": "NH1" <-> "NH2" Residue "a ARG 80": "NH1" <-> "NH2" Residue "c ARG 170": "NH1" <-> "NH2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 63": "NH1" <-> "NH2" Residue "o ARG 278": "NH1" <-> "NH2" Residue "o TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 396": "NH1" <-> "NH2" Residue "y ARG 110": "NH1" <-> "NH2" Residue "b ARG 11": "NH1" <-> "NH2" Residue "f ARG 82": "NH1" <-> "NH2" Residue "g ARG 30": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "j ARG 97": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 58929 Number of models: 1 Model: "" Number of chains: 36 Chain: "I" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 714 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 13, 'rna3p_pyr': 18} Link IDs: {'rna2p': 3, 'rna3p': 30} Chain breaks: 1 Chain: "E" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 346 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 10} Chain: "2" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1025 Classifications: {'RNA': 49} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 15, 'rna3p_pyr': 26} Link IDs: {'rna2p': 8, 'rna3p': 40} Chain: "6" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2108 Classifications: {'RNA': 99} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 12, 'rna3p_pur': 45, 'rna3p_pyr': 34} Link IDs: {'rna2p': 20, 'rna3p': 78} Chain breaks: 1 Chain: "5" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2999 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 7, 'rna3p_pur': 59, 'rna3p_pyr': 61} Link IDs: {'rna2p': 20, 'rna3p': 120} Chain breaks: 2 Chain: "A" Number of atoms: 15199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1914, 15199 Classifications: {'peptide': 1914} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 162} Link IDs: {'PCIS': 2, 'PTRANS': 98, 'TRANS': 1813} Chain breaks: 3 Unresolved non-hydrogen bonds: 604 Unresolved non-hydrogen angles: 747 Unresolved non-hydrogen dihedrals: 469 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 28, 'PHE:plan': 1, 'GLU:plan': 69, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 459 Chain: "C" Number of atoms: 6562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6562 Classifications: {'peptide': 874} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 49, 'TRANS': 824} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 438 Unresolved non-hydrogen angles: 528 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 1, 'GLU:plan': 37, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 280 Chain: "H" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3261 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 394} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2690 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain: "K" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1458 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "L" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1162 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 150} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 76 Chain: "M" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2016 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 241} 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: "N" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1798 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1755 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 1 Chain: "P" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 565 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 614 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain breaks: 1 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 9, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 13, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 173 Chain: "S" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3229 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 8, 'TRANS': 459} Chain breaks: 14 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 853 Unresolved non-hydrogen angles: 1096 Unresolved non-hydrogen dihedrals: 742 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 17, 'ASN:plan1': 5, 'TRP:plan': 8, 'ASP:plan': 12, 'PHE:plan': 11, 'GLU:plan': 25, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 513 Chain: "T" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 1684 Classifications: {'peptide': 338} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 307} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 13 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1155 Unresolved non-hydrogen angles: 1495 Unresolved non-hydrogen dihedrals: 976 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'UNK:plan-1': 18, 'TYR:plan': 16, 'ASN:plan1': 11, 'TRP:plan': 9, 'ASP:plan': 11, 'PHE:plan': 16, 'GLU:plan': 35, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 655 Chain: "a" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1119 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 786 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'GLU:plan': 8, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 60 Chain: "o" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2425 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 296} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "X" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 338 Classifications: {'peptide': 68} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 66} Link IDs: {'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 68} Unresolved non-hydrogen planarities: 68 Chain: "y" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 679 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain breaks: 2 Chain: "b" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 631 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "d" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 573 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "h" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "j" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "6" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 2, ' MG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 37170 SG CYS L 104 119.572 159.622 55.145 1.00 75.41 S ATOM 37176 SG CYS L 105 116.218 159.636 57.619 1.00 94.62 S ATOM 37201 SG CYS L 108 119.316 156.956 57.042 1.00 75.02 S ATOM 37481 SG CYS L 148 117.163 157.670 54.259 1.00 84.39 S ATOM 37170 SG CYS L 104 119.572 159.622 55.145 1.00 75.41 S ATOM 37300 SG CYS L 122 122.565 156.429 55.032 1.00 79.14 S ATOM 37491 SG CYS L 150 120.985 158.015 52.098 1.00 83.92 S ATOM 37506 SG CYS L 153 122.563 160.191 54.033 1.00108.43 S ATOM 37201 SG CYS L 108 119.316 156.956 57.042 1.00 75.02 S ATOM 37286 SG CYS L 120 121.751 154.131 56.547 1.00 81.56 S ATOM 37300 SG CYS L 122 122.565 156.429 55.032 1.00 79.14 S ATOM 37458 SG CYS L 145 118.892 154.002 54.771 1.00 99.48 S ATOM 38091 SG CYS M 73 111.787 135.605 43.452 1.00 81.57 S ATOM 38153 SG CYS M 81 110.505 138.634 41.803 1.00 83.60 S ATOM 38193 SG CYS M 87 113.773 138.819 44.049 1.00106.84 S ATOM 39775 SG CYS N 34 114.684 121.535 69.008 1.00 79.22 S ATOM 39798 SG CYS N 37 114.780 119.622 71.558 1.00 94.61 S ATOM 39997 SG CYS N 61 117.804 121.307 71.827 1.00 90.51 S ATOM 40021 SG CYS N 64 117.609 118.493 70.140 1.00101.83 S ATOM 39617 SG CYS N 13 130.577 123.842 61.112 1.00136.95 S ATOM 39641 SG CYS N 16 127.770 126.378 59.960 1.00150.78 S ATOM 40075 SG CYS N 71 126.934 123.725 62.872 1.00119.28 S ATOM 40096 SG CYS N 74 127.840 123.931 59.418 1.00120.09 S Time building chain proxies: 22.68, per 1000 atoms: 0.38 Number of scatterers: 58929 At special positions: 0 Unit cell: (190.19, 260.26, 201.63, 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 6 29.99 K 2 19.00 S 192 16.00 P 348 15.00 Mg 3 11.99 O 11753 8.00 N 10406 7.00 C 36219 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: 19.52 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L1000 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 104 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 148 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 108 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 105 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 104 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 150 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 122 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 153 " pdb=" ZN L1002 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 108 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 122 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 120 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 145 " pdb=" ZN M1000 " pdb="ZN ZN M1000 " - pdb=" NE2 HIS M 91 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 73 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 87 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 81 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 34 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 64 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 61 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 71 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 16 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 74 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 13 " Number of angles added : 33 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 258 helices and 55 sheets defined 45.4% alpha, 8.2% beta 99 base pairs and 168 stacking pairs defined. Time for finding SS restraints: 17.91 Creating SS restraints... Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 156 through 177 removed outlier: 4.397A pdb=" N LYS A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 210 through 230 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 305 through 317 Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 388 through 391 No H-bonds generated for 'chain 'A' and resid 388 through 391' Processing helix chain 'A' and resid 473 through 481 removed outlier: 3.883A pdb=" N SER A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 516 through 534 Processing helix chain 'A' and resid 547 through 553 Processing helix chain 'A' and resid 564 through 586 Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 619 through 640 Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 660 through 663 No H-bonds generated for 'chain 'A' and resid 660 through 663' Processing helix chain 'A' and resid 666 through 669 No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 671 through 691 removed outlier: 4.011A pdb=" N TYR A 688 " --> pdb=" O HIS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 734 Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 750 through 769 Processing helix chain 'A' and resid 776 through 795 removed outlier: 3.705A pdb=" N THR A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 836 Processing helix chain 'A' and resid 842 through 869 Processing helix chain 'A' and resid 876 through 893 Processing helix chain 'A' and resid 908 through 925 removed outlier: 3.717A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 945 Processing helix chain 'A' and resid 947 through 960 Processing helix chain 'A' and resid 986 through 1006 removed outlier: 3.714A pdb=" N THR A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1034 Processing helix chain 'A' and resid 1063 through 1073 Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1109 through 1135 removed outlier: 3.940A pdb=" N GLY A1127 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLN A1128 " --> pdb=" O LEU A1125 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU A1129 " --> pdb=" O LEU A1126 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG A1130 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A1131 " --> pdb=" O GLN A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1155 Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'A' and resid 1217 through 1233 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1306 through 1320 Processing helix chain 'A' and resid 1328 through 1345 Processing helix chain 'A' and resid 1348 through 1350 No H-bonds generated for 'chain 'A' and resid 1348 through 1350' Processing helix chain 'A' and resid 1354 through 1374 Processing helix chain 'A' and resid 1386 through 1389 No H-bonds generated for 'chain 'A' and resid 1386 through 1389' Processing helix chain 'A' and resid 1392 through 1394 No H-bonds generated for 'chain 'A' and resid 1392 through 1394' Processing helix chain 'A' and resid 1412 through 1415 No H-bonds generated for 'chain 'A' and resid 1412 through 1415' Processing helix chain 'A' and resid 1441 through 1443 No H-bonds generated for 'chain 'A' and resid 1441 through 1443' Processing helix chain 'A' and resid 1447 through 1471 Processing helix chain 'A' and resid 1483 through 1485 No H-bonds generated for 'chain 'A' and resid 1483 through 1485' Processing helix chain 'A' and resid 1491 through 1494 Processing helix chain 'A' and resid 1499 through 1504 removed outlier: 5.396A pdb=" N TYR A1504 " --> pdb=" O HIS A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1515 Processing helix chain 'A' and resid 1530 through 1533 No H-bonds generated for 'chain 'A' and resid 1530 through 1533' Processing helix chain 'A' and resid 1540 through 1549 Processing helix chain 'A' and resid 1552 through 1559 removed outlier: 4.180A pdb=" N GLU A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N HIS A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1565 No H-bonds generated for 'chain 'A' and resid 1562 through 1565' Processing helix chain 'A' and resid 1571 through 1573 No H-bonds generated for 'chain 'A' and resid 1571 through 1573' Processing helix chain 'A' and resid 1602 through 1609 removed outlier: 3.857A pdb=" N PHE A1606 " --> pdb=" O PRO A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1614 No H-bonds generated for 'chain 'A' and resid 1611 through 1614' Processing helix chain 'A' and resid 1639 through 1648 Processing helix chain 'A' and resid 1653 through 1671 Processing helix chain 'A' and resid 1688 through 1691 Processing helix chain 'A' and resid 1749 through 1759 Processing helix chain 'A' and resid 1795 through 1808 Processing helix chain 'A' and resid 1810 through 1822 Processing helix chain 'A' and resid 1841 through 1843 No H-bonds generated for 'chain 'A' and resid 1841 through 1843' Processing helix chain 'A' and resid 1896 through 1900 Processing helix chain 'A' and resid 1905 through 1923 removed outlier: 3.668A pdb=" N LYS A1910 " --> pdb=" O SER A1906 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1950 removed outlier: 3.807A pdb=" N VAL A1946 " --> pdb=" O ASP A1942 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASP A1950 " --> pdb=" O VAL A1946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1967 through 1970 Processing helix chain 'A' and resid 1972 through 1980 Processing helix chain 'A' and resid 1994 through 1998 Processing helix chain 'A' and resid 2001 through 2017 Processing helix chain 'A' and resid 2019 through 2026 Processing helix chain 'A' and resid 2045 through 2066 Processing helix chain 'A' and resid 2075 through 2083 Processing helix chain 'A' and resid 2091 through 2099 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 166 through 170 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 221 through 231 Processing helix chain 'C' and resid 247 through 259 Processing helix chain 'C' and resid 270 through 275 Processing helix chain 'C' and resid 281 through 298 Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'C' and resid 339 through 348 removed outlier: 3.878A pdb=" N ASP C 342 " --> pdb=" O SER C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 378 through 390 Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 410 through 414 removed outlier: 3.860A pdb=" N GLN C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 410 through 414' Processing helix chain 'C' and resid 417 through 428 Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 447 through 456 removed outlier: 3.548A pdb=" N ASP C 450 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 508 through 514 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 612 through 628 Proline residue: C 616 - end of helix Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 717 through 724 removed outlier: 3.600A pdb=" N GLN C 721 " --> pdb=" O SER C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 755 Processing helix chain 'C' and resid 760 through 764 Processing helix chain 'C' and resid 782 through 785 No H-bonds generated for 'chain 'C' and resid 782 through 785' Processing helix chain 'C' and resid 793 through 804 Processing helix chain 'C' and resid 831 through 852 Proline residue: C 840 - end of helix Processing helix chain 'C' and resid 870 through 882 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 914 through 921 Processing helix chain 'C' and resid 962 through 974 Processing helix chain 'C' and resid 991 through 996 Processing helix chain 'H' and resid 12 through 31 Proline residue: H 27 - end of helix removed outlier: 3.826A pdb=" N SER H 30 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 removed outlier: 4.092A pdb=" N LEU H 37 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN H 38 " --> pdb=" O ASP H 35 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU H 39 " --> pdb=" O ASN H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'H' and resid 72 through 86 Processing helix chain 'H' and resid 88 through 107 Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'H' and resid 134 through 144 Processing helix chain 'H' and resid 152 through 164 removed outlier: 5.808A pdb=" N TRP H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 182 Processing helix chain 'H' and resid 188 through 203 removed outlier: 3.681A pdb=" N LYS H 203 " --> pdb=" O GLU H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 261 removed outlier: 3.810A pdb=" N THR H 252 " --> pdb=" O PHE H 248 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA H 254 " --> pdb=" O GLU H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 301 Processing helix chain 'H' and resid 305 through 314 Processing helix chain 'H' and resid 322 through 335 Processing helix chain 'H' and resid 341 through 353 Processing helix chain 'H' and resid 355 through 370 Processing helix chain 'H' and resid 372 through 375 Processing helix chain 'H' and resid 378 through 392 Processing helix chain 'H' and resid 416 through 430 Processing helix chain 'H' and resid 433 through 442 Processing helix chain 'H' and resid 458 through 467 Processing helix chain 'H' and resid 473 through 480 Processing helix chain 'J' and resid 111 through 120 Processing helix chain 'K' and resid 40 through 42 No H-bonds generated for 'chain 'K' and resid 40 through 42' Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'K' and resid 88 through 91 Processing helix chain 'K' and resid 154 through 163 Proline residue: K 160 - end of helix Processing helix chain 'K' and resid 182 through 185 No H-bonds generated for 'chain 'K' and resid 182 through 185' Processing helix chain 'K' and resid 201 through 224 Processing helix chain 'L' and resid 14 through 33 removed outlier: 3.715A pdb=" N GLU L 17 " --> pdb=" O ASP L 14 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS L 18 " --> pdb=" O GLY L 15 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS L 20 " --> pdb=" O GLU L 17 " (cutoff:3.500A) Proline residue: L 21 - end of helix removed outlier: 3.691A pdb=" N THR L 24 " --> pdb=" O PRO L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 67 Processing helix chain 'L' and resid 75 through 84 Processing helix chain 'L' and resid 89 through 96 Processing helix chain 'L' and resid 106 through 109 Processing helix chain 'L' and resid 121 through 123 No H-bonds generated for 'chain 'L' and resid 121 through 123' Processing helix chain 'L' and resid 126 through 136 Processing helix chain 'M' and resid 55 through 58 No H-bonds generated for 'chain 'M' and resid 55 through 58' Processing helix chain 'M' and resid 63 through 67 Processing helix chain 'M' and resid 74 through 78 Processing helix chain 'M' and resid 84 through 86 No H-bonds generated for 'chain 'M' and resid 84 through 86' Processing helix chain 'M' and resid 96 through 102 Processing helix chain 'M' and resid 105 through 107 No H-bonds generated for 'chain 'M' and resid 105 through 107' Processing helix chain 'M' and resid 142 through 145 No H-bonds generated for 'chain 'M' and resid 142 through 145' Processing helix chain 'M' and resid 153 through 167 removed outlier: 3.655A pdb=" N ARG M 166 " --> pdb=" O PHE M 162 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU M 167 " --> pdb=" O VAL M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 198 Processing helix chain 'M' and resid 232 through 253 removed outlier: 4.182A pdb=" N ARG M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 68 Processing helix chain 'N' and resid 84 through 93 Processing helix chain 'N' and resid 107 through 115 removed outlier: 4.013A pdb=" N ARG N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 127 removed outlier: 4.287A pdb=" N ILE N 125 " --> pdb=" O GLY N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 143 Processing helix chain 'N' and resid 216 through 225 Processing helix chain 'N' and resid 256 through 265 Processing helix chain 'N' and resid 307 through 323 Processing helix chain 'O' and resid 15 through 28 Processing helix chain 'O' and resid 33 through 39 Processing helix chain 'O' and resid 45 through 54 Processing helix chain 'O' and resid 67 through 79 Processing helix chain 'O' and resid 84 through 91 Processing helix chain 'O' and resid 95 through 106 Processing helix chain 'O' and resid 145 through 159 Processing helix chain 'O' and resid 165 through 194 Processing helix chain 'O' and resid 231 through 250 Processing helix chain 'P' and resid 15 through 19 Processing helix chain 'P' and resid 164 through 172 Processing helix chain 'R' and resid 11 through 14 No H-bonds generated for 'chain 'R' and resid 11 through 14' Processing helix chain 'R' and resid 26 through 30 Processing helix chain 'R' and resid 37 through 46 removed outlier: 3.589A pdb=" N GLN R 43 " --> pdb=" O ARG R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 86 Processing helix chain 'R' and resid 92 through 115 Processing helix chain 'S' and resid 40 through 60 Processing helix chain 'S' and resid 65 through 78 Processing helix chain 'S' and resid 81 through 94 Processing helix chain 'S' and resid 99 through 111 Processing helix chain 'S' and resid 115 through 128 Processing helix chain 'S' and resid 133 through 146 Processing helix chain 'S' and resid 149 through 162 Processing helix chain 'S' and resid 166 through 178 Processing helix chain 'S' and resid 185 through 195 Processing helix chain 'S' and resid 199 through 211 Processing helix chain 'S' and resid 215 through 231 Processing helix chain 'S' and resid 240 through 256 Processing helix chain 'S' and resid 260 through 273 Processing helix chain 'S' and resid 278 through 290 Processing helix chain 'S' and resid 296 through 314 Processing helix chain 'S' and resid 321 through 331 Processing helix chain 'S' and resid 335 through 348 Processing helix chain 'S' and resid 357 through 376 Processing helix chain 'S' and resid 382 through 394 Processing helix chain 'S' and resid 404 through 415 Processing helix chain 'S' and resid 420 through 431 removed outlier: 3.562A pdb=" N LYS S 425 " --> pdb=" O PRO S 421 " (cutoff:3.500A) Processing helix chain 'S' and resid 440 through 449 Processing helix chain 'S' and resid 453 through 466 Processing helix chain 'S' and resid 471 through 482 Processing helix chain 'S' and resid 486 through 499 Processing helix chain 'S' and resid 508 through 520 Processing helix chain 'S' and resid 531 through 540 Processing helix chain 'S' and resid 546 through 555 Processing helix chain 'T' and resid 408 through 419 removed outlier: 3.877A pdb=" N LYS T 419 " --> pdb=" O VAL T 415 " (cutoff:3.500A) Processing helix chain 'T' and resid 425 through 434 Processing helix chain 'T' and resid 436 through 439 No H-bonds generated for 'chain 'T' and resid 436 through 439' Processing helix chain 'T' and resid 450 through 460 Processing helix chain 'T' and resid 463 through 474 Processing helix chain 'T' and resid 484 through 496 removed outlier: 3.517A pdb=" N ARG T 494 " --> pdb=" O ASN T 490 " (cutoff:3.500A) Processing helix chain 'T' and resid 503 through 522 Proline residue: T 515 - end of helix Proline residue: T 518 - end of helix Processing helix chain 'T' and resid 542 through 554 Processing helix chain 'T' and resid 567 through 580 Processing helix chain 'T' and resid 586 through 596 Processing helix chain 'T' and resid 602 through 613 Proline residue: T 613 - end of helix Processing helix chain 'T' and resid 619 through 633 Processing helix chain 'T' and resid 642 through 654 Processing helix chain 'T' and resid 662 through 676 Processing helix chain 'T' and resid 681 through 692 Processing helix chain 'T' and resid 703 through 718 Processing helix chain 'T' and resid 724 through 734 Processing helix chain 'T' and resid 740 through 754 Processing helix chain 'T' and resid 759 through 770 Processing helix chain 'T' and resid 778 through 789 Processing helix chain 'T' and resid 1001 through 1016 Processing helix chain 'a' and resid 77 through 88 Processing helix chain 'a' and resid 107 through 126 Processing helix chain 'a' and resid 134 through 152 removed outlier: 4.052A pdb=" N ASP a 138 " --> pdb=" O GLU a 134 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS a 141 " --> pdb=" O LEU a 137 " (cutoff:3.500A) Proline residue: a 145 - end of helix removed outlier: 3.746A pdb=" N ARG a 152 " --> pdb=" O LEU a 148 " (cutoff:3.500A) Processing helix chain 'a' and resid 157 through 171 removed outlier: 3.558A pdb=" N SER a 162 " --> pdb=" O ASP a 158 " (cutoff:3.500A) Processing helix chain 'a' and resid 176 through 187 Processing helix chain 'a' and resid 226 through 245 Processing helix chain 'c' and resid 167 through 171 Processing helix chain 'c' and resid 180 through 195 removed outlier: 3.588A pdb=" N ASP c 192 " --> pdb=" O LYS c 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 218 through 223 Processing helix chain 'c' and resid 295 through 312 Processing helix chain 'c' and resid 325 through 328 No H-bonds generated for 'chain 'c' and resid 325 through 328' Processing helix chain 'c' and resid 334 through 347 removed outlier: 3.711A pdb=" N LEU c 339 " --> pdb=" O TYR c 336 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS c 342 " --> pdb=" O LEU c 339 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN c 345 " --> pdb=" O LYS c 342 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU c 346 " --> pdb=" O ARG c 343 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 59 Processing helix chain 'o' and resid 277 through 282 Processing helix chain 'X' and resid 7 through 14 Processing helix chain 'X' and resid 17 through 25 Processing helix chain 'X' and resid 93 through 128 removed outlier: 4.649A pdb=" N UNK X 107 " --> pdb=" O UNK X 103 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N UNK X 108 " --> pdb=" O UNK X 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N UNK X 117 " --> pdb=" O UNK X 113 " (cutoff:3.500A) Processing helix chain 'y' and resid 97 through 113 Processing helix chain 'y' and resid 158 through 183 Processing helix chain 'y' and resid 198 through 208 removed outlier: 3.509A pdb=" N GLN y 202 " --> pdb=" O ASP y 198 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 15 No H-bonds generated for 'chain 'b' and resid 13 through 15' Processing helix chain 'd' and resid 6 through 13 Processing helix chain 'd' and resid 66 through 68 No H-bonds generated for 'chain 'd' and resid 66 through 68' Processing helix chain 'e' and resid 13 through 23 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'f' and resid 15 through 22 Processing helix chain 'h' and resid 3 through 9 Processing helix chain 'h' and resid 103 through 107 Processing helix chain 'j' and resid 16 through 28 Processing helix chain 'j' and resid 30 through 40 removed outlier: 3.994A pdb=" N ILE j 34 " --> pdb=" O MET j 31 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA j 37 " --> pdb=" O ILE j 34 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR j 40 " --> pdb=" O ALA j 37 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 188 through 194 Processing sheet with id= B, first strand: chain 'A' and resid 591 through 593 Processing sheet with id= C, first strand: chain 'A' and resid 968 through 972 Processing sheet with id= D, first strand: chain 'A' and resid 1167 through 1174 Processing sheet with id= E, first strand: chain 'A' and resid 1257 through 1262 removed outlier: 6.935A pdb=" N LEU A1288 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS A1299 " --> pdb=" O TRP A1286 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP A1286 " --> pdb=" O LYS A1299 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1406 through 1408 Processing sheet with id= G, first strand: chain 'A' and resid 1624 through 1626 Processing sheet with id= H, first strand: chain 'A' and resid 1731 through 1734 Processing sheet with id= I, first strand: chain 'A' and resid 1773 through 1778 Processing sheet with id= J, first strand: chain 'A' and resid 1880 through 1882 removed outlier: 6.166A pdb=" N GLN A1932 " --> pdb=" O LEU A1850 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL A1852 " --> pdb=" O GLN A1932 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A1934 " --> pdb=" O VAL A1852 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A1955 " --> pdb=" O ILE A1933 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL A1935 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG A1957 " --> pdb=" O VAL A1935 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1859 through 1864 removed outlier: 4.560A pdb=" N ARG A1859 " --> pdb=" O ILE A1875 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 133 through 135 removed outlier: 8.931A pdb=" N ILE C 134 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET C 209 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 240 removed outlier: 6.327A pdb=" N VAL C 266 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE C 312 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 500 through 503 removed outlier: 4.357A pdb=" N LEU C 468 " --> pdb=" O SER C 579 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP C 469 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER C 490 " --> pdb=" O TRP C 469 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS C 471 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE C 488 " --> pdb=" O HIS C 471 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 474 through 476 Processing sheet with id= P, first strand: chain 'C' and resid 492 through 494 Processing sheet with id= Q, first strand: chain 'C' and resid 543 through 545 Processing sheet with id= R, first strand: chain 'C' and resid 642 through 646 Processing sheet with id= S, first strand: chain 'C' and resid 678 through 681 Processing sheet with id= T, first strand: chain 'C' and resid 775 through 777 removed outlier: 6.395A pdb=" N SER C 709 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 928 through 931 removed outlier: 4.035A pdb=" N LYS C 890 " --> pdb=" O ARG C 903 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLN C 905 " --> pdb=" O ILE C 888 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE C 888 " --> pdb=" O GLN C 905 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 144 through 147 removed outlier: 6.462A pdb=" N ASP J 168 " --> pdb=" O LEU J 174 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU J 174 " --> pdb=" O ASP J 168 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 185 through 190 removed outlier: 6.953A pdb=" N VAL J 200 " --> pdb=" O ARG J 186 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL J 188 " --> pdb=" O PHE J 198 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE J 198 " --> pdb=" O VAL J 188 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL J 190 " --> pdb=" O TYR J 196 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR J 196 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASP J 210 " --> pdb=" O ILE J 216 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE J 216 " --> pdb=" O ASP J 210 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 227 through 232 removed outlier: 6.902A pdb=" N ALA J 242 " --> pdb=" O ARG J 228 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL J 230 " --> pdb=" O ALA J 240 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA J 240 " --> pdb=" O VAL J 230 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE J 232 " --> pdb=" O LEU J 238 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU J 238 " --> pdb=" O ILE J 232 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY J 243 " --> pdb=" O VAL J 247 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL J 247 " --> pdb=" O GLY J 243 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE J 248 " --> pdb=" O LEU J 262 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP J 252 " --> pdb=" O PRO J 258 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 271 through 274 removed outlier: 4.668A pdb=" N VAL J 281 " --> pdb=" O TRP J 293 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP J 294 " --> pdb=" O THR J 300 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THR J 300 " --> pdb=" O ASP J 294 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 314 through 316 Processing sheet with id= AA, first strand: chain 'J' and resid 363 through 367 removed outlier: 3.958A pdb=" N ALA J 366 " --> pdb=" O SER J 374 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP J 377 " --> pdb=" O LYS J 383 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS J 383 " --> pdb=" O ASP J 377 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 129 through 133 removed outlier: 6.641A pdb=" N ILE J 425 " --> pdb=" O SER J 132 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 333 through 335 removed outlier: 4.791A pdb=" N GLY J 335 " --> pdb=" O LEU J 341 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU J 341 " --> pdb=" O GLY J 335 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 222 through 225 removed outlier: 3.778A pdb=" N LEU M 137 " --> pdb=" O VAL M 184 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 26 through 28 Processing sheet with id= AF, first strand: chain 'N' and resid 206 through 208 removed outlier: 4.138A pdb=" N PHE N 206 " --> pdb=" O PRO N 292 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE N 290 " --> pdb=" O TYR N 208 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'o' and resid 156 through 158 removed outlier: 4.241A pdb=" N LYS o 450 " --> pdb=" O GLY o 446 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'o' and resid 177 through 179 Processing sheet with id= AI, first strand: chain 'o' and resid 230 through 234 removed outlier: 3.692A pdb=" N ALA o 211 " --> pdb=" O SER o 224 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'o' and resid 252 through 255 removed outlier: 3.637A pdb=" N ASP o 252 " --> pdb=" O GLY o 266 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'o' and resid 339 through 342 removed outlier: 3.503A pdb=" N MET o 339 " --> pdb=" O GLN o 354 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'o' and resid 385 through 388 removed outlier: 4.341A pdb=" N TYR o 385 " --> pdb=" O GLY o 401 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'y' and resid 144 through 146 Processing sheet with id= AN, first strand: chain 'b' and resid 80 through 83 removed outlier: 6.183A pdb=" N CYS b 48 " --> pdb=" O LEU b 82 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ARG b 21 " --> pdb=" O VAL b 97 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N VAL b 97 " --> pdb=" O ARG b 21 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU b 23 " --> pdb=" O THR b 95 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR b 95 " --> pdb=" O LEU b 23 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'b' and resid 43 through 45 Processing sheet with id= AP, first strand: chain 'd' and resid 69 through 73 removed outlier: 7.059A pdb=" N GLU d 22 " --> pdb=" O LYS d 70 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE d 72 " --> pdb=" O SER d 20 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER d 20 " --> pdb=" O ILE d 72 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN d 43 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'd' and resid 48 through 50 Processing sheet with id= AR, first strand: chain 'e' and resid 26 through 30 Processing sheet with id= AS, first strand: chain 'e' and resid 52 through 54 removed outlier: 4.090A pdb=" N VAL e 52 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU e 82 " --> pdb=" O VAL e 52 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'f' and resid 71 through 73 removed outlier: 3.865A pdb=" N GLN f 52 " --> pdb=" O SER f 44 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER f 44 " --> pdb=" O GLN f 52 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN f 54 " --> pdb=" O LEU f 42 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU f 42 " --> pdb=" O ASN f 54 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'f' and resid 28 through 31 Processing sheet with id= AV, first strand: chain 'g' and resid 23 through 25 Processing sheet with id= AW, first strand: chain 'g' and resid 38 through 41 Processing sheet with id= AX, first strand: chain 'h' and resid 24 through 26 Processing sheet with id= AY, first strand: chain 'h' and resid 84 through 87 removed outlier: 6.637A pdb=" N THR h 41 " --> pdb=" O LEU h 29 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU h 29 " --> pdb=" O THR h 41 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'h' and resid 16 through 19 Processing sheet with id= BA, first strand: chain 'j' and resid 67 through 70 Processing sheet with id= BB, first strand: chain 'j' and resid 72 through 77 Processing sheet with id= BC, first strand: chain 'j' and resid 44 through 48 removed outlier: 3.907A pdb=" N VAL j 103 " --> pdb=" O SER j 47 " (cutoff:3.500A) 2288 hydrogen bonds defined for protein. 6375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 236 hydrogen bonds 416 hydrogen bond angles 0 basepair planarities 99 basepair parallelities 168 stacking parallelities Total time for adding SS restraints: 33.90 Time building geometry restraints manager: 21.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 8927 1.31 - 1.44: 17815 1.44 - 1.57: 33015 1.57 - 1.70: 683 1.70 - 1.82: 315 Bond restraints: 60755 Sorted by residual: bond pdb=" C SER c 230 " pdb=" O SER c 230 " ideal model delta sigma weight residual 1.231 1.345 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C HIS A1658 " pdb=" O HIS A1658 " ideal model delta sigma weight residual 1.236 1.302 -0.065 1.15e-02 7.56e+03 3.23e+01 bond pdb=" CA PRO e 12 " pdb=" C PRO e 12 " ideal model delta sigma weight residual 1.514 1.546 -0.031 5.50e-03 3.31e+04 3.22e+01 bond pdb=" CD GLN C 251 " pdb=" OE1 GLN C 251 " ideal model delta sigma weight residual 1.231 1.332 -0.101 1.90e-02 2.77e+03 2.84e+01 bond pdb=" ND1 HIS A 194 " pdb=" CE1 HIS A 194 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.79e+01 ... (remaining 60750 not shown) Histogram of bond angle deviations from ideal: 95.93 - 104.08: 1989 104.08 - 112.22: 29026 112.22 - 120.37: 28218 120.37 - 128.52: 23888 128.52 - 136.66: 908 Bond angle restraints: 84029 Sorted by residual: angle pdb=" C ILE T 612 " pdb=" N PRO T 613 " pdb=" CA PRO T 613 " ideal model delta sigma weight residual 119.19 132.68 -13.49 1.06e+00 8.90e-01 1.62e+02 angle pdb=" CA VAL T 514 " pdb=" C VAL T 514 " pdb=" N PRO T 515 " ideal model delta sigma weight residual 120.83 114.65 6.18 6.10e-01 2.69e+00 1.03e+02 angle pdb=" C PHE T 615 " pdb=" N PRO T 616 " pdb=" CA PRO T 616 " ideal model delta sigma weight residual 120.38 130.57 -10.19 1.03e+00 9.43e-01 9.79e+01 angle pdb=" C4' G 5 27 " pdb=" C3' G 5 27 " pdb=" O3' G 5 27 " ideal model delta sigma weight residual 109.40 121.53 -12.13 1.50e+00 4.44e-01 6.54e+01 angle pdb=" C ASP T 436 " pdb=" N PRO T 437 " pdb=" CA PRO T 437 " ideal model delta sigma weight residual 119.28 128.15 -8.87 1.10e+00 8.26e-01 6.50e+01 ... (remaining 84024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 34865 35.47 - 70.93: 887 70.93 - 106.40: 58 106.40 - 141.86: 11 141.86 - 177.33: 6 Dihedral angle restraints: 35827 sinusoidal: 15875 harmonic: 19952 Sorted by residual: dihedral pdb=" O4' C 5 79 " pdb=" C1' C 5 79 " pdb=" N1 C 5 79 " pdb=" C2 C 5 79 " ideal model delta sinusoidal sigma weight residual 200.00 68.37 131.63 1 1.50e+01 4.44e-03 7.10e+01 dihedral pdb=" O4' U E -9 " pdb=" C1' U E -9 " pdb=" N1 U E -9 " pdb=" C2 U E -9 " ideal model delta sinusoidal sigma weight residual 232.00 83.87 148.13 1 1.70e+01 3.46e-03 6.14e+01 dihedral pdb=" CA ILE C 105 " pdb=" C ILE C 105 " pdb=" N PHE C 106 " pdb=" CA PHE C 106 " ideal model delta harmonic sigma weight residual -180.00 -144.34 -35.66 0 5.00e+00 4.00e-02 5.09e+01 ... (remaining 35824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.990: 9965 0.990 - 1.980: 0 1.980 - 2.970: 0 2.970 - 3.961: 0 3.961 - 4.951: 2 Chirality restraints: 9967 Sorted by residual: chirality pdb=" C2 IHP A3001 " pdb=" C1 IHP A3001 " pdb=" C3 IHP A3001 " pdb=" O12 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.52 2.43 -4.95 2.00e-01 2.50e+01 6.13e+02 chirality pdb=" C3 IHP A3001 " pdb=" C2 IHP A3001 " pdb=" C4 IHP A3001 " pdb=" O13 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.34 2.45 -4.79 2.00e-01 2.50e+01 5.74e+02 chirality pdb=" C3' C 6 92 " pdb=" C4' C 6 92 " pdb=" O3' C 6 92 " pdb=" C2' C 6 92 " both_signs ideal model delta sigma weight residual False -2.74 -2.01 -0.73 2.00e-01 2.50e+01 1.35e+01 ... (remaining 9964 not shown) Planarity restraints: 9414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE H 73 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO H 74 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO H 74 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO H 74 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 379 " -0.062 5.00e-02 4.00e+02 9.37e-02 1.41e+01 pdb=" N PRO C 380 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO C 380 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 380 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G 5 32 " -0.022 2.00e-02 2.50e+03 2.13e-02 1.36e+01 pdb=" N9 G 5 32 " 0.001 2.00e-02 2.50e+03 pdb=" C8 G 5 32 " 0.008 2.00e-02 2.50e+03 pdb=" N7 G 5 32 " 0.009 2.00e-02 2.50e+03 pdb=" C5 G 5 32 " 0.010 2.00e-02 2.50e+03 pdb=" C6 G 5 32 " 0.011 2.00e-02 2.50e+03 pdb=" O6 G 5 32 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G 5 32 " -0.048 2.00e-02 2.50e+03 pdb=" C2 G 5 32 " 0.046 2.00e-02 2.50e+03 pdb=" N2 G 5 32 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 5 32 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G 5 32 " -0.003 2.00e-02 2.50e+03 ... (remaining 9411 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.21: 11 2.21 - 2.94: 24243 2.94 - 3.68: 112692 3.68 - 4.41: 178517 4.41 - 5.14: 275286 Nonbonded interactions: 590749 Sorted by model distance: nonbonded pdb=" N1 A 5 45 " pdb=" O4 U 5 74 " model vdw 1.479 2.496 nonbonded pdb=" P G I 1 " pdb=" O2' A I 70 " model vdw 1.619 3.400 nonbonded pdb=" O LYS H 311 " pdb=" CD2 LEU H 315 " model vdw 1.854 3.460 nonbonded pdb=" OP1 G 6 78 " pdb="MG MG 61001 " model vdw 2.100 2.170 nonbonded pdb=" OP2 U 6 80 " pdb="MG MG 61001 " model vdw 2.100 2.170 ... (remaining 590744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 17.910 Check model and map are aligned: 0.640 Set scattering table: 0.390 Process input model: 146.670 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.114 60755 Z= 0.551 Angle : 1.406 13.862 84029 Z= 0.986 Chirality : 0.110 4.951 9967 Planarity : 0.006 0.108 9414 Dihedral : 15.519 177.326 22807 Min Nonbonded Distance : 1.479 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.54 % Favored : 90.57 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.09), residues: 6554 helix: 0.22 (0.08), residues: 3058 sheet: -3.25 (0.16), residues: 682 loop : -2.81 (0.10), residues: 2814 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1497 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1369 time to evaluate : 4.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 128 outliers final: 39 residues processed: 1464 average time/residue: 0.6004 time to fit residues: 1462.0371 Evaluate side-chains 784 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 745 time to evaluate : 4.910 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.5114 time to fit residues: 41.8827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 591 optimal weight: 8.9990 chunk 530 optimal weight: 20.0000 chunk 294 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 357 optimal weight: 0.7980 chunk 283 optimal weight: 6.9990 chunk 548 optimal weight: 7.9990 chunk 212 optimal weight: 0.9990 chunk 333 optimal weight: 1.9990 chunk 408 optimal weight: 3.9990 chunk 635 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN A 344 ASN A 404 ASN A 509 HIS ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 ASN A1030 GLN A1091 ASN A1097 HIS A1140 ASN A1190 ASN A1369 ASN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1508 HIS A1516 GLN A1782 ASN A1856 ASN A2047 GLN C 143 HIS C 158 HIS C 211 ASN C 289 ASN C 290 HIS C 310 ASN C 358 ASN C 403 ASN C 431 GLN C 511 GLN C 557 HIS C 683 ASN C 764 ASN C 776 ASN H 320 ASN J 270 ASN ** J 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN K 86 ASN K 140 ASN K 192 ASN K 195 ASN L 115 ASN L 116 ASN ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 ASN N 225 GLN O 15 ASN O 26 GLN ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 161 ASN O 197 ASN P 34 HIS P 158 ASN S 47 GLN S 147 ASN ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 233 GLN ** S 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 248 ASN a 99 GLN a 149 GLN ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 183 ASN c 304 GLN ** o 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 185 ASN ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 33 GLN b 40 HIS ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 24 ASN f 47 ASN g 66 ASN ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 50 ASN j 64 HIS Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 60755 Z= 0.304 Angle : 0.761 20.836 84029 Z= 0.381 Chirality : 0.045 0.481 9967 Planarity : 0.005 0.066 9414 Dihedral : 14.040 174.278 11326 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.39 % Favored : 94.55 % Rotamer Outliers : 4.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.80 (0.10), residues: 6554 helix: 1.41 (0.09), residues: 3084 sheet: -2.72 (0.16), residues: 765 loop : -2.24 (0.11), residues: 2705 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 883 time to evaluate : 5.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 211 outliers final: 87 residues processed: 1029 average time/residue: 0.5307 time to fit residues: 953.2859 Evaluate side-chains 750 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 663 time to evaluate : 4.903 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 0.4303 time to fit residues: 77.3488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 353 optimal weight: 0.8980 chunk 197 optimal weight: 0.0980 chunk 529 optimal weight: 6.9990 chunk 432 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 chunk 636 optimal weight: 10.0000 chunk 687 optimal weight: 20.0000 chunk 567 optimal weight: 10.0000 chunk 631 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 510 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 733 GLN ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN A1424 HIS ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2018 ASN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 GLN ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN H 425 GLN ** J 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN O 83 GLN P 167 GLN a 171 GLN ** c 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 348 GLN ** y 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN g 66 ASN ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 66 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 60755 Z= 0.213 Angle : 0.677 17.771 84029 Z= 0.337 Chirality : 0.042 0.443 9967 Planarity : 0.005 0.065 9414 Dihedral : 13.718 174.868 11326 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.25 % Favored : 94.72 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 6554 helix: 1.71 (0.09), residues: 3094 sheet: -2.40 (0.17), residues: 774 loop : -1.99 (0.12), residues: 2686 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 812 time to evaluate : 4.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 68 residues processed: 927 average time/residue: 0.5624 time to fit residues: 910.8006 Evaluate side-chains 717 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 649 time to evaluate : 4.984 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.4725 time to fit residues: 66.6121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 629 optimal weight: 0.9980 chunk 478 optimal weight: 7.9990 chunk 330 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 303 optimal weight: 7.9990 chunk 427 optimal weight: 6.9990 chunk 639 optimal weight: 0.8980 chunk 676 optimal weight: 3.9990 chunk 333 optimal weight: 0.0870 chunk 605 optimal weight: 0.7980 chunk 182 optimal weight: 20.0000 overall best weight: 1.3560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2018 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 425 GLN ** J 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN K 194 ASN ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 GLN ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 304 GLN ** o 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 ASN ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 60755 Z= 0.220 Angle : 0.662 17.348 84029 Z= 0.326 Chirality : 0.041 0.354 9967 Planarity : 0.004 0.063 9414 Dihedral : 13.559 173.790 11326 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.71 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.11), residues: 6554 helix: 1.70 (0.09), residues: 3088 sheet: -2.16 (0.17), residues: 769 loop : -1.88 (0.12), residues: 2697 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 719 time to evaluate : 5.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 58 residues processed: 817 average time/residue: 0.5466 time to fit residues: 777.6198 Evaluate side-chains 682 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 624 time to evaluate : 5.801 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.4718 time to fit residues: 57.5592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 563 optimal weight: 0.7980 chunk 384 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 503 optimal weight: 0.9990 chunk 279 optimal weight: 0.4980 chunk 577 optimal weight: 30.0000 chunk 467 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 345 optimal weight: 20.0000 chunk 607 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 ASN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2018 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 171 ASN ** K 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 GLN ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 23 GLN ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 50 ASN ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 60755 Z= 0.298 Angle : 0.669 17.542 84029 Z= 0.334 Chirality : 0.041 0.313 9967 Planarity : 0.005 0.069 9414 Dihedral : 13.548 174.502 11326 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.87 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.11), residues: 6554 helix: 1.69 (0.09), residues: 3096 sheet: -1.97 (0.17), residues: 768 loop : -1.82 (0.12), residues: 2690 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 673 time to evaluate : 5.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 66 residues processed: 778 average time/residue: 0.5385 time to fit residues: 733.9704 Evaluate side-chains 678 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 612 time to evaluate : 4.898 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.4370 time to fit residues: 61.2818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 227 optimal weight: 8.9990 chunk 609 optimal weight: 4.9990 chunk 133 optimal weight: 0.0870 chunk 397 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 677 optimal weight: 0.3980 chunk 562 optimal weight: 30.0000 chunk 313 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 224 optimal weight: 0.9980 chunk 355 optimal weight: 3.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2018 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 390 HIS ** J 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 67 GLN S 170 ASN ** a 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 144 GLN ** y 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 ASN ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 60755 Z= 0.181 Angle : 0.645 16.221 84029 Z= 0.315 Chirality : 0.040 0.313 9967 Planarity : 0.004 0.067 9414 Dihedral : 13.405 172.917 11326 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.13 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 6554 helix: 1.78 (0.09), residues: 3082 sheet: -1.79 (0.18), residues: 756 loop : -1.72 (0.12), residues: 2716 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 723 time to evaluate : 4.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 32 residues processed: 779 average time/residue: 0.5823 time to fit residues: 797.8381 Evaluate side-chains 669 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 637 time to evaluate : 4.972 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4499 time to fit residues: 34.4456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 652 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 385 optimal weight: 2.9990 chunk 494 optimal weight: 0.0970 chunk 383 optimal weight: 8.9990 chunk 570 optimal weight: 40.0000 chunk 378 optimal weight: 0.8980 chunk 674 optimal weight: 3.9990 chunk 422 optimal weight: 0.9990 chunk 411 optimal weight: 2.9990 chunk 311 optimal weight: 0.3980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2018 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 162 ASN ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 71 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 60755 Z= 0.198 Angle : 0.646 16.173 84029 Z= 0.315 Chirality : 0.040 0.401 9967 Planarity : 0.004 0.070 9414 Dihedral : 13.292 173.284 11326 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.31 % Favored : 94.64 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.11), residues: 6554 helix: 1.84 (0.09), residues: 3089 sheet: -1.65 (0.18), residues: 751 loop : -1.63 (0.12), residues: 2714 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 702 time to evaluate : 4.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 26 residues processed: 751 average time/residue: 0.5438 time to fit residues: 715.9803 Evaluate side-chains 667 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 641 time to evaluate : 4.934 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4717 time to fit residues: 29.2010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 417 optimal weight: 0.9980 chunk 269 optimal weight: 1.9990 chunk 402 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 130 optimal weight: 0.1980 chunk 428 optimal weight: 5.9990 chunk 459 optimal weight: 6.9990 chunk 333 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 530 optimal weight: 10.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2018 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 GLN N 72 GLN N 81 HIS ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 154 GLN ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 300 ASN ** c 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 60755 Z= 0.227 Angle : 0.654 16.293 84029 Z= 0.319 Chirality : 0.040 0.344 9967 Planarity : 0.004 0.067 9414 Dihedral : 13.275 173.615 11326 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.11), residues: 6554 helix: 1.86 (0.09), residues: 3077 sheet: -1.56 (0.18), residues: 746 loop : -1.56 (0.12), residues: 2731 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 681 time to evaluate : 5.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 36 residues processed: 723 average time/residue: 0.5542 time to fit residues: 703.3464 Evaluate side-chains 670 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 634 time to evaluate : 4.957 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4384 time to fit residues: 37.0086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 613 optimal weight: 5.9990 chunk 646 optimal weight: 3.9990 chunk 589 optimal weight: 2.9990 chunk 628 optimal weight: 0.0670 chunk 378 optimal weight: 8.9990 chunk 273 optimal weight: 2.9990 chunk 493 optimal weight: 20.0000 chunk 192 optimal weight: 0.8980 chunk 568 optimal weight: 40.0000 chunk 594 optimal weight: 2.9990 chunk 626 optimal weight: 7.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN H 105 GLN H 425 GLN ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 287 GLN ** d 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 60755 Z= 0.249 Angle : 0.669 18.573 84029 Z= 0.327 Chirality : 0.041 0.352 9967 Planarity : 0.004 0.070 9414 Dihedral : 13.282 174.089 11326 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.11), residues: 6554 helix: 1.84 (0.09), residues: 3086 sheet: -1.48 (0.18), residues: 745 loop : -1.50 (0.12), residues: 2723 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 656 time to evaluate : 5.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 25 residues processed: 687 average time/residue: 0.5656 time to fit residues: 680.5544 Evaluate side-chains 650 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 625 time to evaluate : 4.993 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.4593 time to fit residues: 28.0365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 412 optimal weight: 2.9990 chunk 664 optimal weight: 20.0000 chunk 405 optimal weight: 0.7980 chunk 315 optimal weight: 0.9980 chunk 462 optimal weight: 1.9990 chunk 697 optimal weight: 0.9990 chunk 641 optimal weight: 10.0000 chunk 555 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 428 optimal weight: 7.9990 chunk 340 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 HIS ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN N 22 ASN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 283 GLN ** o 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 60755 Z= 0.216 Angle : 0.673 16.278 84029 Z= 0.326 Chirality : 0.041 0.427 9967 Planarity : 0.004 0.067 9414 Dihedral : 13.229 173.744 11326 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.42 % Favored : 94.54 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.11), residues: 6554 helix: 1.84 (0.09), residues: 3085 sheet: -1.40 (0.19), residues: 745 loop : -1.50 (0.12), residues: 2724 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13108 Ramachandran restraints generated. 6554 Oldfield, 0 Emsley, 6554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 668 time to evaluate : 5.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 677 average time/residue: 0.5659 time to fit residues: 678.0542 Evaluate side-chains 633 residues out of total 6082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 622 time to evaluate : 4.929 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4435 time to fit residues: 15.9075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 441 optimal weight: 0.9980 chunk 591 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 512 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 556 optimal weight: 0.0010 chunk 232 optimal weight: 0.8980 chunk 571 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN ** a 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 304 GLN ** c 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.088266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.068178 restraints weight = 237273.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069410 restraints weight = 122093.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.069635 restraints weight = 74506.394| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 60755 Z= 0.206 Angle : 0.679 16.092 84029 Z= 0.327 Chirality : 0.041 0.379 9967 Planarity : 0.004 0.070 9414 Dihedral : 13.166 173.527 11326 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 6554 helix: 1.81 (0.09), residues: 3091 sheet: -1.36 (0.19), residues: 742 loop : -1.50 (0.12), residues: 2721 =============================================================================== Job complete usr+sys time: 12823.64 seconds wall clock time: 227 minutes 17.98 seconds (13637.98 seconds total)