Starting phenix.real_space_refine (version: dev) on Thu Feb 23 09:50:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwf_13680/02_2023/7pwf_13680_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwf_13680/02_2023/7pwf_13680.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwf_13680/02_2023/7pwf_13680_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwf_13680/02_2023/7pwf_13680_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwf_13680/02_2023/7pwf_13680_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwf_13680/02_2023/7pwf_13680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwf_13680/02_2023/7pwf_13680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwf_13680/02_2023/7pwf_13680_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwf_13680/02_2023/7pwf_13680_updated.pdb" } resolution = 2.85 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "d GLU 91": "OE1" <-> "OE2" Residue "d ARG 100": "NH1" <-> "NH2" Residue "d ARG 121": "NH1" <-> "NH2" Residue "d PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 41": "NH1" <-> "NH2" Residue "T ARG 46": "NH1" <-> "NH2" Residue "T ARG 77": "NH1" <-> "NH2" Residue "T ARG 94": "NH1" <-> "NH2" Residue "T ARG 118": "NH1" <-> "NH2" Residue "N ARG 3": "NH1" <-> "NH2" Residue "N GLU 119": "OE1" <-> "OE2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J ARG 42": "NH1" <-> "NH2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "J GLU 90": "OE1" <-> "OE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "X ARG 14": "NH1" <-> "NH2" Residue "X ARG 28": "NH1" <-> "NH2" Residue "X GLU 99": "OE1" <-> "OE2" Residue "X PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 29": "OE1" <-> "OE2" Residue "S ARG 41": "NH1" <-> "NH2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S GLU 66": "OE1" <-> "OE2" Residue "S GLU 93": "OE1" <-> "OE2" Residue "Q ARG 58": "NH1" <-> "NH2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "Q GLU 114": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "Y GLU 3": "OE1" <-> "OE2" Residue "Y GLU 34": "OE1" <-> "OE2" Residue "Y GLU 37": "OE1" <-> "OE2" Residue "Y GLU 86": "OE1" <-> "OE2" Residue "b GLU 55": "OE1" <-> "OE2" Residue "b GLU 56": "OE1" <-> "OE2" Residue "b GLU 75": "OE1" <-> "OE2" Residue "a ARG 28": "NH1" <-> "NH2" Residue "a TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 68": "NH1" <-> "NH2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "P GLU 21": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P ARG 44": "NH1" <-> "NH2" Residue "P PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 106": "OE1" <-> "OE2" Residue "R GLU 22": "OE1" <-> "OE2" Residue "R GLU 79": "OE1" <-> "OE2" Residue "R GLU 80": "OE1" <-> "OE2" Residue "K GLU 41": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 131": "OE1" <-> "OE2" Residue "I ARG 144": "NH1" <-> "NH2" Residue "e ARG 15": "NH1" <-> "NH2" Residue "e ARG 31": "NH1" <-> "NH2" Residue "H GLU 20": "OE1" <-> "OE2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H ARG 99": "NH1" <-> "NH2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "H ARG 116": "NH1" <-> "NH2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "H ARG 120": "NH1" <-> "NH2" Residue "H ARG 143": "NH1" <-> "NH2" Residue "H ARG 153": "NH1" <-> "NH2" Residue "H ARG 169": "NH1" <-> "NH2" Residue "H GLU 182": "OE1" <-> "OE2" Residue "H ARG 183": "NH1" <-> "NH2" Residue "n ARG 2": "NH1" <-> "NH2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "c ARG 8": "NH1" <-> "NH2" Residue "c ARG 15": "NH1" <-> "NH2" Residue "O ARG 44": "NH1" <-> "NH2" Residue "O GLU 45": "OE1" <-> "OE2" Residue "O ARG 49": "NH1" <-> "NH2" Residue "O ARG 58": "NH1" <-> "NH2" Residue "O ARG 82": "NH1" <-> "NH2" Residue "O ARG 92": "NH1" <-> "NH2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "O ARG 140": "NH1" <-> "NH2" Residue "W GLU 36": "OE1" <-> "OE2" Residue "W ARG 97": "NH1" <-> "NH2" Residue "W PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 115": "OE1" <-> "OE2" Residue "E ARG 145": "NH1" <-> "NH2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E GLU 252": "OE1" <-> "OE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L GLU 49": "OE1" <-> "OE2" Residue "L GLU 163": "OE1" <-> "OE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L GLU 191": "OE1" <-> "OE2" Residue "U GLU 40": "OE1" <-> "OE2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U GLU 77": "OE1" <-> "OE2" Residue "U GLU 121": "OE1" <-> "OE2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 138": "NH1" <-> "NH2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G ARG 193": "NH1" <-> "NH2" Residue "G GLU 223": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 122": "NH1" <-> "NH2" Residue "F TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F GLU 157": "OE1" <-> "OE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 190": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 60466 Number of models: 1 Model: "" Number of chains: 45 Chain: "d" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 398 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "T" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 934 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 124} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "N" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1198 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 141} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1322 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 161} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1402 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "X" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1104 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 4, 'TRANS': 137} Chain: "S" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1055 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "Q" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1641 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 9, 'TRANS': 202} Chain: "A" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain: "Y" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 708 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "b" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 614 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 72} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "a" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 785 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 419 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 58} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 31 Chain: "V" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 605 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 79} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 836 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 780 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 689 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1282 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain breaks: 1 Chain: "e" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 291 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1194 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain breaks: 6 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 84 Chain: "n" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 217 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "c" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 439 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain breaks: 1 Chain: "O" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 935 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "W" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1031 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 124} Chain: "E" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2058 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 241} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "2" Number of atoms: 29096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1355, 29096 Classifications: {'RNA': 1355} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 92, 'rna3p': 13, 'rna3p_pur': 606, 'rna3p_pyr': 530} Link IDs: {'rna2p': 203, 'rna3p': 1151} Chain breaks: 19 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Chain: "L" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1481 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 171} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "U" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 609 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain breaks: 2 Chain: "G" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1530 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 4 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1246 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 154} Chain breaks: 1 Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' K': 7, ' MG': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' K': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 274 Unusual residues: {' K': 239, ' MG': 35} Classifications: {'undetermined': 274} Link IDs: {None: 273} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.40, per 1000 atoms: 0.44 Number of scatterers: 60466 At special positions: 0 Unit cell: (226.95, 186.15, 216.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 266 19.00 S 173 16.00 P 1355 15.00 Mg 37 11.99 O 14810 8.00 N 11250 7.00 C 32575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 97 " - pdb=" SG CYS b 100 " distance=2.04 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: 22.70 Conformation dependent library (CDL) restraints added in 4.0 seconds 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 141 helices and 44 sheets defined 30.7% alpha, 14.9% beta 364 base pairs and 743 stacking pairs defined. Time for finding SS restraints: 20.70 Creating SS restraints... Processing helix chain 'd' and resid 114 through 116 No H-bonds generated for 'chain 'd' and resid 114 through 116' Processing helix chain 'd' and resid 121 through 126 removed outlier: 3.779A pdb=" N LYS d 125 " --> pdb=" O ARG d 121 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU d 126 " --> pdb=" O ARG d 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 121 through 126' Processing helix chain 'd' and resid 128 through 131 No H-bonds generated for 'chain 'd' and resid 128 through 131' Processing helix chain 'T' and resid 9 through 21 removed outlier: 3.535A pdb=" N ILE T 13 " --> pdb=" O ALA T 9 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN T 14 " --> pdb=" O ASP T 10 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA T 18 " --> pdb=" O ASN T 14 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS T 19 " --> pdb=" O SER T 15 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS T 21 " --> pdb=" O ALA T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 64 removed outlier: 3.621A pdb=" N ILE T 64 " --> pdb=" O ARG T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 76 No H-bonds generated for 'chain 'T' and resid 73 through 76' Processing helix chain 'T' and resid 97 through 111 removed outlier: 4.778A pdb=" N GLN T 110 " --> pdb=" O GLN T 106 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS T 111 " --> pdb=" O PHE T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 131 removed outlier: 6.111A pdb=" N MET T 129 " --> pdb=" O ASN T 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 42 removed outlier: 3.910A pdb=" N GLU N 35 " --> pdb=" O GLU N 31 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 57 removed outlier: 3.688A pdb=" N GLY N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 71 through 77 Processing helix chain 'N' and resid 86 through 102 Processing helix chain 'N' and resid 109 through 131 Processing helix chain 'N' and resid 146 through 151 removed outlier: 3.857A pdb=" N LEU N 150 " --> pdb=" O ALA N 146 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA N 151 " --> pdb=" O ALA N 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 146 through 151' Processing helix chain 'J' and resid 4 through 7 Processing helix chain 'J' and resid 23 through 35 removed outlier: 3.656A pdb=" N LEU J 30 " --> pdb=" O LEU J 26 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU J 32 " --> pdb=" O ALA J 28 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS J 33 " --> pdb=" O GLU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 62 removed outlier: 4.193A pdb=" N ARG J 46 " --> pdb=" O GLU J 43 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS J 53 " --> pdb=" O MET J 50 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG J 55 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR J 57 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA J 58 " --> pdb=" O ARG J 55 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG J 59 " --> pdb=" O ARG J 56 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU J 62 " --> pdb=" O ARG J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 84 removed outlier: 4.185A pdb=" N ALA J 76 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET J 84 " --> pdb=" O ARG J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'J' and resid 103 through 109 removed outlier: 4.197A pdb=" N ARG J 109 " --> pdb=" O ASP J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 117 removed outlier: 3.641A pdb=" N VAL J 116 " --> pdb=" O GLN J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 132 Processing helix chain 'J' and resid 152 through 154 No H-bonds generated for 'chain 'J' and resid 152 through 154' Processing helix chain 'D' and resid 14 through 37 removed outlier: 3.909A pdb=" N ASN D 19 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 25 " --> pdb=" O CYS D 21 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 67 through 75 removed outlier: 5.995A pdb=" N ARG D 71 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS D 73 " --> pdb=" O TYR D 70 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS D 74 " --> pdb=" O ARG D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 114 removed outlier: 3.524A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 135 Processing helix chain 'D' and resid 168 through 171 Processing helix chain 'X' and resid 10 through 23 removed outlier: 4.412A pdb=" N TRP X 22 " --> pdb=" O ARG X 18 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA X 23 " --> pdb=" O VAL X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 31 Processing helix chain 'X' and resid 34 through 38 Processing helix chain 'X' and resid 90 through 93 Processing helix chain 'X' and resid 130 through 134 Processing helix chain 'S' and resid 28 through 34 removed outlier: 4.230A pdb=" N VAL S 33 " --> pdb=" O GLU S 29 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY S 34 " --> pdb=" O CYS S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 46 Processing helix chain 'S' and resid 48 through 50 No H-bonds generated for 'chain 'S' and resid 48 through 50' Processing helix chain 'S' and resid 63 through 73 Processing helix chain 'S' and resid 106 through 119 removed outlier: 3.981A pdb=" N LEU S 116 " --> pdb=" O ASP S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 128 Processing helix chain 'Q' and resid 54 through 56 No H-bonds generated for 'chain 'Q' and resid 54 through 56' Processing helix chain 'Q' and resid 68 through 72 Processing helix chain 'Q' and resid 92 through 108 removed outlier: 3.832A pdb=" N SER Q 104 " --> pdb=" O ARG Q 100 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL Q 107 " --> pdb=" O ILE Q 103 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU Q 108 " --> pdb=" O SER Q 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 125 removed outlier: 3.847A pdb=" N ARG Q 121 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA Q 122 " --> pdb=" O SER Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 131 No H-bonds generated for 'chain 'Q' and resid 129 through 131' Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 45 through 50 Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.672A pdb=" N PHE C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 129 Processing helix chain 'C' and resid 176 through 184 removed outlier: 3.653A pdb=" N LYS C 180 " --> pdb=" O PRO C 176 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 216 removed outlier: 3.976A pdb=" N SER C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TYR C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 56 through 72 removed outlier: 4.679A pdb=" N THR A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 86 through 99 removed outlier: 4.566A pdb=" N ARG A 90 " --> pdb=" O PRO A 86 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ALA A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.703A pdb=" N SER A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 191 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'B' and resid 21 through 24 Processing helix chain 'B' and resid 55 through 58 No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 68 through 71 No H-bonds generated for 'chain 'B' and resid 68 through 71' Processing helix chain 'B' and resid 76 through 81 removed outlier: 5.735A pdb=" N ASN B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 113 removed outlier: 3.706A pdb=" N LEU B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 175 removed outlier: 3.624A pdb=" N MET B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 194 through 202 removed outlier: 4.092A pdb=" N GLU B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'Y' and resid 36 through 41 removed outlier: 4.962A pdb=" N ALA Y 41 " --> pdb=" O GLU Y 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 80 through 85 Processing helix chain 'Y' and resid 90 through 93 No H-bonds generated for 'chain 'Y' and resid 90 through 93' Processing helix chain 'b' and resid 48 through 50 No H-bonds generated for 'chain 'b' and resid 48 through 50' Processing helix chain 'b' and resid 53 through 57 Processing helix chain 'a' and resid 47 through 49 No H-bonds generated for 'chain 'a' and resid 47 through 49' Processing helix chain 'a' and resid 52 through 55 No H-bonds generated for 'chain 'a' and resid 52 through 55' Processing helix chain 'a' and resid 75 through 80 Processing helix chain 'a' and resid 91 through 93 No H-bonds generated for 'chain 'a' and resid 91 through 93' Processing helix chain 'Z' and resid 27 through 32 Processing helix chain 'Z' and resid 42 through 48 Processing helix chain 'Z' and resid 54 through 64 removed outlier: 3.622A pdb=" N MET Z 60 " --> pdb=" O ALA Z 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG Z 61 " --> pdb=" O LYS Z 57 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN Z 62 " --> pdb=" O ARG Z 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 65 through 69 Processing helix chain 'V' and resid 73 through 83 removed outlier: 3.773A pdb=" N MET V 78 " --> pdb=" O ASP V 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 24 No H-bonds generated for 'chain 'P' and resid 22 through 24' Processing helix chain 'P' and resid 39 through 45 Processing helix chain 'P' and resid 54 through 60 Processing helix chain 'P' and resid 109 through 111 No H-bonds generated for 'chain 'P' and resid 109 through 111' Processing helix chain 'P' and resid 116 through 118 No H-bonds generated for 'chain 'P' and resid 116 through 118' Processing helix chain 'R' and resid 7 through 19 removed outlier: 3.544A pdb=" N ALA R 12 " --> pdb=" O THR R 8 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS R 15 " --> pdb=" O ARG R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 34 Processing helix chain 'R' and resid 47 through 64 removed outlier: 3.627A pdb=" N THR R 59 " --> pdb=" O GLY R 55 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 84 removed outlier: 4.057A pdb=" N GLU R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG R 81 " --> pdb=" O GLN R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 110 Processing helix chain 'K' and resid 4 through 12 removed outlier: 3.799A pdb=" N ALA K 11 " --> pdb=" O ALA K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 63 removed outlier: 3.598A pdb=" N ILE K 56 " --> pdb=" O HIS K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 91 removed outlier: 3.728A pdb=" N GLN K 85 " --> pdb=" O GLU K 81 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS K 89 " --> pdb=" O GLN K 85 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU K 90 " --> pdb=" O PHE K 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 9 No H-bonds generated for 'chain 'I' and resid 7 through 9' Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 99 through 102 No H-bonds generated for 'chain 'I' and resid 99 through 102' Processing helix chain 'I' and resid 117 through 122 removed outlier: 4.438A pdb=" N SER I 121 " --> pdb=" O PRO I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 137 removed outlier: 4.480A pdb=" N GLN I 135 " --> pdb=" O GLU I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 152 No H-bonds generated for 'chain 'I' and resid 149 through 152' Processing helix chain 'I' and resid 163 through 171 Processing helix chain 'e' and resid 13 through 17 Processing helix chain 'e' and resid 33 through 43 Processing helix chain 'H' and resid 22 through 27 Processing helix chain 'H' and resid 67 through 73 removed outlier: 6.077A pdb=" N GLN H 71 " --> pdb=" O PRO H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 82 removed outlier: 3.873A pdb=" N LEU H 82 " --> pdb=" O GLU H 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 78 through 82' Processing helix chain 'H' and resid 118 through 120 No H-bonds generated for 'chain 'H' and resid 118 through 120' Processing helix chain 'H' and resid 122 through 134 removed outlier: 3.578A pdb=" N ASN H 127 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU H 130 " --> pdb=" O TYR H 126 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP H 131 " --> pdb=" O ASN H 127 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N CYS H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 167 through 181 removed outlier: 3.932A pdb=" N THR H 170 " --> pdb=" O SER H 167 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LYS H 171 " --> pdb=" O GLU H 168 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR H 181 " --> pdb=" O LYS H 178 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 22 Processing helix chain 'O' and resid 52 through 54 No H-bonds generated for 'chain 'O' and resid 52 through 54' Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 65 through 81 removed outlier: 3.613A pdb=" N ASP O 74 " --> pdb=" O GLN O 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU O 77 " --> pdb=" O GLN O 73 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP O 81 " --> pdb=" O GLU O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 116 removed outlier: 3.642A pdb=" N ILE O 110 " --> pdb=" O GLY O 106 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY O 116 " --> pdb=" O ALA O 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 20 Processing helix chain 'W' and resid 32 through 44 Processing helix chain 'W' and resid 86 through 93 removed outlier: 4.330A pdb=" N ASN W 92 " --> pdb=" O LYS W 88 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 118 Processing helix chain 'E' and resid 11 through 13 No H-bonds generated for 'chain 'E' and resid 11 through 13' Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 44 through 48 Processing helix chain 'E' and resid 58 through 66 removed outlier: 3.624A pdb=" N MET E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 247 through 255 Processing helix chain 'L' and resid 30 through 47 removed outlier: 4.617A pdb=" N GLU L 35 " --> pdb=" O ARG L 31 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG L 36 " --> pdb=" O ARG L 32 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA L 37 " --> pdb=" O ALA L 33 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 93 No H-bonds generated for 'chain 'L' and resid 90 through 93' Processing helix chain 'U' and resid 36 through 46 Processing helix chain 'G' and resid 145 through 149 removed outlier: 4.219A pdb=" N ARG G 149 " --> pdb=" O LYS G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 230 removed outlier: 3.597A pdb=" N GLU G 212 " --> pdb=" O ALA G 208 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET G 214 " --> pdb=" O LYS G 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 51 Processing helix chain 'F' and resid 54 through 62 Processing helix chain 'F' and resid 72 through 86 removed outlier: 3.603A pdb=" N LYS F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU F 84 " --> pdb=" O GLY F 80 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU F 85 " --> pdb=" O GLU F 81 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 129 through 148 Processing helix chain 'F' and resid 155 through 168 removed outlier: 3.506A pdb=" N GLU F 161 " --> pdb=" O GLU F 157 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA F 168 " --> pdb=" O MET F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 189 Processing sheet with id= A, first strand: chain 'T' and resid 81 through 83 removed outlier: 3.529A pdb=" N SER T 81 " --> pdb=" O LYS T 93 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N HIS T 91 " --> pdb=" O GLN T 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'T' and resid 113 through 115 Processing sheet with id= C, first strand: chain 'J' and resid 136 through 138 Processing sheet with id= D, first strand: chain 'D' and resid 92 through 94 removed outlier: 5.876A pdb=" N VAL D 54 " --> pdb=" O TRP D 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER D 42 " --> pdb=" O GLN D 57 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 153 through 161 removed outlier: 3.566A pdb=" N ARG D 154 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY D 146 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'X' and resid 80 through 84 removed outlier: 3.748A pdb=" N GLN X 53 " --> pdb=" O ARG X 71 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ALA X 103 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL X 122 " --> pdb=" O ALA X 103 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'S' and resid 15 through 17 Processing sheet with id= H, first strand: chain 'Q' and resid 25 through 30 Processing sheet with id= I, first strand: chain 'C' and resid 105 through 112 removed outlier: 3.578A pdb=" N ASN C 76 " --> pdb=" O HIS C 95 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE C 97 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL C 74 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLY C 99 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLU C 72 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 152 through 156 Processing sheet with id= K, first strand: chain 'A' and resid 102 through 104 removed outlier: 6.393A pdb=" N LEU A 126 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL A 82 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU A 128 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A 129 " --> pdb=" O PRO A 148 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 150 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 164 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N CYS A 153 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE A 166 " --> pdb=" O CYS A 153 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 43 through 46 removed outlier: 7.057A pdb=" N VAL A 53 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.817A pdb=" N LEU B 90 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N CYS B 96 " --> pdb=" O TRP B 27 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY B 42 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 63 through 67 removed outlier: 5.511A pdb=" N GLN B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N PHE B 100 " --> pdb=" O GLN B 87 " (cutoff:3.500A) removed outlier: 14.001A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.193A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N HIS B 101 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 134 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'Y' and resid 5 through 9 removed outlier: 3.703A pdb=" N THR Y 5 " --> pdb=" O LEU Y 27 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'Y' and resid 12 through 14 Processing sheet with id= Q, first strand: chain 'b' and resid 73 through 77 Processing sheet with id= R, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= S, first strand: chain 'a' and resid 36 through 43 Processing sheet with id= T, first strand: chain 'Z' and resid 68 through 72 removed outlier: 3.504A pdb=" N ILE Z 71 " --> pdb=" O THR Z 79 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR Z 79 " --> pdb=" O ILE Z 71 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'V' and resid 40 through 44 Processing sheet with id= V, first strand: chain 'P' and resid 76 through 78 removed outlier: 4.238A pdb=" N VAL P 76 " --> pdb=" O THR P 93 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 66 through 70 Processing sheet with id= X, first strand: chain 'I' and resid 52 through 56 Processing sheet with id= Y, first strand: chain 'I' and resid 72 through 77 Processing sheet with id= Z, first strand: chain 'I' and resid 157 through 159 removed outlier: 6.443A pdb=" N ASP I 115 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE I 88 " --> pdb=" O ASP I 115 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 95 through 97 removed outlier: 5.963A pdb=" N VAL H 63 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR H 64 " --> pdb=" O SER H 48 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER H 48 " --> pdb=" O TYR H 64 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 107 through 109 removed outlier: 3.856A pdb=" N LYS H 112 " --> pdb=" O THR H 109 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 141 through 145 removed outlier: 3.771A pdb=" N GLY H 141 " --> pdb=" O VAL H 157 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'c' and resid 5 through 8 Processing sheet with id= AE, first strand: chain 'c' and resid 38 through 41 Processing sheet with id= AF, first strand: chain 'O' and resid 46 through 51 removed outlier: 6.745A pdb=" N VAL O 38 " --> pdb=" O ILE O 47 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG O 49 " --> pdb=" O ILE O 36 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE O 36 " --> pdb=" O ARG O 49 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER O 51 " --> pdb=" O THR O 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR O 34 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA O 86 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N CYS O 25 " --> pdb=" O ALA O 86 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N HIS O 88 " --> pdb=" O CYS O 25 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE O 27 " --> pdb=" O HIS O 88 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS O 90 " --> pdb=" O ILE O 27 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ALA O 29 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG O 92 " --> pdb=" O ALA O 29 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'W' and resid 24 through 27 Processing sheet with id= AH, first strand: chain 'W' and resid 71 through 74 removed outlier: 6.909A pdb=" N ILE W 103 " --> pdb=" O ILE W 126 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR W 128 " --> pdb=" O HIS W 101 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N HIS W 101 " --> pdb=" O TYR W 128 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 89 through 92 Processing sheet with id= AJ, first strand: chain 'E' and resid 121 through 125 removed outlier: 3.762A pdb=" N GLU E 171 " --> pdb=" O LYS E 161 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE E 169 " --> pdb=" O ASN E 163 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 146 through 148 Processing sheet with id= AL, first strand: chain 'E' and resid 225 through 227 removed outlier: 6.385A pdb=" N ARG E 209 " --> pdb=" O GLN E 196 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE E 198 " --> pdb=" O MET E 207 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET E 207 " --> pdb=" O ILE E 198 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 143 through 154 removed outlier: 3.536A pdb=" N SER L 121 " --> pdb=" O ILE L 129 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ARG L 131 " --> pdb=" O VAL L 119 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL L 119 " --> pdb=" O ARG L 131 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ASP L 133 " --> pdb=" O GLY L 117 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLY L 117 " --> pdb=" O ASP L 133 " (cutoff:3.500A) removed outlier: 15.843A pdb=" N LEU L 135 " --> pdb=" O LEU L 115 " (cutoff:3.500A) removed outlier: 16.831A pdb=" N LEU L 115 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY L 170 " --> pdb=" O VAL L 183 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL L 183 " --> pdb=" O GLY L 170 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'U' and resid 90 through 96 Processing sheet with id= AO, first strand: chain 'U' and resid 65 through 71 Processing sheet with id= AP, first strand: chain 'G' and resid 18 through 23 removed outlier: 3.590A pdb=" N GLY G 60 " --> pdb=" O SER G 116 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL G 118 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE G 58 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 79 through 83 Processing sheet with id= AR, first strand: chain 'F' and resid 109 through 111 920 hydrogen bonds defined for protein. 2526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 988 hydrogen bonds 1710 hydrogen bond angles 0 basepair planarities 364 basepair parallelities 743 stacking parallelities Total time for adding SS restraints: 40.58 Time building geometry restraints manager: 24.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 6201 1.29 - 1.43: 25134 1.43 - 1.56: 29796 1.56 - 1.69: 2694 1.69 - 1.83: 264 Bond restraints: 64089 Sorted by residual: bond pdb=" C2' 4AC 21426 " pdb=" C1' 4AC 21426 " ideal model delta sigma weight residual 1.529 1.311 0.218 1.50e-02 4.44e+03 2.11e+02 bond pdb=" O4' 4AC 21426 " pdb=" C1' 4AC 21426 " ideal model delta sigma weight residual 1.412 1.623 -0.211 1.50e-02 4.44e+03 1.98e+02 bond pdb=" C2' A2M 2 348 " pdb=" C1' A2M 2 348 " ideal model delta sigma weight residual 1.277 1.538 -0.261 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C2' A2M 2 87 " pdb=" C1' A2M 2 87 " ideal model delta sigma weight residual 1.277 1.538 -0.261 2.00e-02 2.50e+03 1.71e+02 bond pdb=" O4' A2M 2 348 " pdb=" C1' A2M 2 348 " ideal model delta sigma weight residual 1.557 1.301 0.256 2.00e-02 2.50e+03 1.63e+02 ... (remaining 64084 not shown) Histogram of bond angle deviations from ideal: 97.14 - 105.35: 6784 105.35 - 113.56: 39487 113.56 - 121.78: 32815 121.78 - 129.99: 13273 129.99 - 138.21: 785 Bond angle restraints: 93144 Sorted by residual: angle pdb=" C3' C 2 175 " pdb=" O3' C 2 175 " pdb=" P C 2 176 " ideal model delta sigma weight residual 120.20 101.60 18.60 1.50e+00 4.44e-01 1.54e+02 angle pdb=" C3' G 21132 " pdb=" O3' G 21132 " pdb=" P G 21133 " ideal model delta sigma weight residual 120.20 105.85 14.35 1.50e+00 4.44e-01 9.15e+01 angle pdb=" C3' M7A 21390 " pdb=" O3' M7A 21390 " pdb=" P G 21391 " ideal model delta sigma weight residual 120.20 106.02 14.18 1.50e+00 4.44e-01 8.94e+01 angle pdb=" C3' C 2 363 " pdb=" O3' C 2 363 " pdb=" P G 2 364 " ideal model delta sigma weight residual 120.20 107.32 12.88 1.50e+00 4.44e-01 7.38e+01 angle pdb=" C3' G 21410 " pdb=" O3' G 21410 " pdb=" P U 21411 " ideal model delta sigma weight residual 120.20 107.42 12.78 1.50e+00 4.44e-01 7.26e+01 ... (remaining 93139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 34134 35.90 - 71.80: 1368 71.80 - 107.69: 101 107.69 - 143.59: 21 143.59 - 179.49: 30 Dihedral angle restraints: 35654 sinusoidal: 24212 harmonic: 11442 Sorted by residual: dihedral pdb=" O4' C 21160 " pdb=" C1' C 21160 " pdb=" N1 C 21160 " pdb=" C2 C 21160 " ideal model delta sinusoidal sigma weight residual 200.00 20.51 179.49 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 2 547 " pdb=" C1' U 2 547 " pdb=" N1 U 2 547 " pdb=" C2 U 2 547 " ideal model delta sinusoidal sigma weight residual 200.00 20.71 179.29 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21199 " pdb=" C1' C 21199 " pdb=" N1 C 21199 " pdb=" C2 C 21199 " ideal model delta sinusoidal sigma weight residual 200.00 23.30 176.70 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 35651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 10802 0.115 - 0.230: 512 0.230 - 0.344: 18 0.344 - 0.459: 160 0.459 - 0.574: 4 Chirality restraints: 11496 Sorted by residual: chirality pdb=" P G 21005 " pdb=" OP1 G 21005 " pdb=" OP2 G 21005 " pdb=" O5' G 21005 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.23e+00 chirality pdb=" P G 2 180 " pdb=" OP1 G 2 180 " pdb=" OP2 G 2 180 " pdb=" O5' G 2 180 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 7.99e+00 chirality pdb=" P C 2 175 " pdb=" OP1 C 2 175 " pdb=" OP2 C 2 175 " pdb=" O5' C 2 175 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.14e+00 ... (remaining 11493 not shown) Planarity restraints: 6769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' M7A 21390 " 0.077 2.00e-02 2.50e+03 6.46e-01 9.39e+03 pdb=" C4' M7A 21390 " 0.478 2.00e-02 2.50e+03 pdb=" O4' M7A 21390 " 0.787 2.00e-02 2.50e+03 pdb=" C3' M7A 21390 " -0.605 2.00e-02 2.50e+03 pdb=" O3' M7A 21390 " -0.658 2.00e-02 2.50e+03 pdb=" C2' M7A 21390 " -0.186 2.00e-02 2.50e+03 pdb=" O2' M7A 21390 " 0.977 2.00e-02 2.50e+03 pdb=" C1' M7A 21390 " 0.171 2.00e-02 2.50e+03 pdb=" N9 M7A 21390 " -1.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' C4J 2 933 " 0.550 2.00e-02 2.50e+03 5.99e-01 8.06e+03 pdb=" C4' C4J 2 933 " -0.285 2.00e-02 2.50e+03 pdb=" O4' C4J 2 933 " 0.472 2.00e-02 2.50e+03 pdb=" C3' C4J 2 933 " -0.794 2.00e-02 2.50e+03 pdb=" O3' C4J 2 933 " -0.574 2.00e-02 2.50e+03 pdb=" C2' C4J 2 933 " -0.107 2.00e-02 2.50e+03 pdb=" O2' C4J 2 933 " 1.099 2.00e-02 2.50e+03 pdb=" C1' C4J 2 933 " 0.251 2.00e-02 2.50e+03 pdb=" C5 C4J 2 933 " -0.612 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' MA6 21434 " -0.034 2.00e-02 2.50e+03 5.97e-01 8.02e+03 pdb=" C4' MA6 21434 " -0.448 2.00e-02 2.50e+03 pdb=" O4' MA6 21434 " -0.715 2.00e-02 2.50e+03 pdb=" C3' MA6 21434 " 0.590 2.00e-02 2.50e+03 pdb=" O3' MA6 21434 " 0.590 2.00e-02 2.50e+03 pdb=" C2' MA6 21434 " 0.213 2.00e-02 2.50e+03 pdb=" O2' MA6 21434 " -0.921 2.00e-02 2.50e+03 pdb=" C1' MA6 21434 " -0.205 2.00e-02 2.50e+03 pdb=" N9 MA6 21434 " 0.929 2.00e-02 2.50e+03 ... (remaining 6766 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.43: 114 2.43 - 3.11: 39704 3.11 - 3.78: 120368 3.78 - 4.46: 192032 4.46 - 5.14: 263892 Nonbonded interactions: 616110 Sorted by model distance: nonbonded pdb=" OP2 A 2 777 " pdb="MG MG 21765 " model vdw 1.748 2.170 nonbonded pdb=" OP2 C 2 291 " pdb="MG MG 21773 " model vdw 1.913 2.170 nonbonded pdb=" OP1 G 21421 " pdb="MG MG 21769 " model vdw 2.071 2.170 nonbonded pdb=" OP1 A 21416 " pdb="MG MG 21769 " model vdw 2.077 2.170 nonbonded pdb=" O4 U 2 947 " pdb="MG MG 21762 " model vdw 2.079 2.170 ... (remaining 616105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 266 8.98 5 P 1355 5.49 5 Mg 37 5.21 5 S 173 5.16 5 C 32575 2.51 5 N 11250 2.21 5 O 14810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 20.570 Check model and map are aligned: 0.870 Process input model: 156.020 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.420 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 197.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.007 0.261 64089 Z= 0.400 Angle : 0.983 22.702 93144 Z= 0.536 Chirality : 0.071 0.574 11496 Planarity : 0.027 0.646 6769 Dihedral : 17.373 179.489 28243 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.30 % Favored : 94.52 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.09 (0.12), residues: 3849 helix: -1.37 (0.14), residues: 1234 sheet: -0.45 (0.20), residues: 656 loop : -1.70 (0.13), residues: 1959 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 652 time to evaluate : 3.446 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 654 average time/residue: 1.5908 time to fit residues: 1309.0549 Evaluate side-chains 575 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 574 time to evaluate : 3.441 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 4.2433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 437 optimal weight: 10.0000 chunk 392 optimal weight: 5.9990 chunk 217 optimal weight: 0.0050 chunk 134 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 406 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 246 optimal weight: 0.9990 chunk 302 optimal weight: 0.8980 chunk 470 optimal weight: 0.5980 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 145 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN B 174 ASN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN I 72 HIS E 66 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 64 GLN ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN F 68 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 64089 Z= 0.166 Angle : 0.809 28.580 93144 Z= 0.424 Chirality : 0.040 0.365 11496 Planarity : 0.007 0.134 6769 Dihedral : 15.946 179.785 20621 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.71 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 3849 helix: -0.72 (0.14), residues: 1252 sheet: -0.22 (0.20), residues: 636 loop : -1.36 (0.13), residues: 1961 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 599 time to evaluate : 3.538 Fit side-chains outliers start: 70 outliers final: 24 residues processed: 618 average time/residue: 1.5996 time to fit residues: 1247.3016 Evaluate side-chains 593 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 569 time to evaluate : 3.472 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 12 residues processed: 15 average time/residue: 0.7615 time to fit residues: 21.8585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 261 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 391 optimal weight: 6.9990 chunk 320 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 471 optimal weight: 6.9990 chunk 509 optimal weight: 2.9990 chunk 419 optimal weight: 10.0000 chunk 467 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 378 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 145 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS C 125 ASN A 84 ASN A 169 ASN B 89 GLN B 174 ASN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN I 72 HIS E 66 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 ASN L 136 HIS ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 64089 Z= 0.297 Angle : 0.882 26.196 93144 Z= 0.460 Chirality : 0.045 0.262 11496 Planarity : 0.008 0.141 6769 Dihedral : 16.039 179.421 20621 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 3849 helix: -0.74 (0.14), residues: 1252 sheet: -0.17 (0.20), residues: 656 loop : -1.39 (0.13), residues: 1941 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 559 time to evaluate : 3.576 Fit side-chains outliers start: 104 outliers final: 54 residues processed: 607 average time/residue: 1.5665 time to fit residues: 1204.6848 Evaluate side-chains 593 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 539 time to evaluate : 3.459 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 27 residues processed: 28 average time/residue: 0.9708 time to fit residues: 42.7762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 465 optimal weight: 0.8980 chunk 354 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 224 optimal weight: 0.9990 chunk 316 optimal weight: 6.9990 chunk 472 optimal weight: 0.3980 chunk 500 optimal weight: 4.9990 chunk 247 optimal weight: 0.6980 chunk 448 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 145 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 ASN B 89 GLN B 174 ASN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN E 69 ASN E 163 ASN L 50 ASN ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 64089 Z= 0.146 Angle : 0.738 22.656 93144 Z= 0.398 Chirality : 0.038 0.254 11496 Planarity : 0.007 0.127 6769 Dihedral : 15.625 179.989 20621 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 3849 helix: -0.28 (0.15), residues: 1253 sheet: -0.08 (0.20), residues: 683 loop : -1.17 (0.14), residues: 1913 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 578 time to evaluate : 3.535 Fit side-chains outliers start: 107 outliers final: 55 residues processed: 634 average time/residue: 1.5821 time to fit residues: 1274.4080 Evaluate side-chains 597 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 542 time to evaluate : 3.532 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 39 residues processed: 19 average time/residue: 0.8666 time to fit residues: 28.6823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 417 optimal weight: 9.9990 chunk 284 optimal weight: 8.9990 chunk 7 optimal weight: 0.5980 chunk 372 optimal weight: 8.9990 chunk 206 optimal weight: 0.7980 chunk 427 optimal weight: 9.9990 chunk 346 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 449 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 overall best weight: 4.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 145 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 ASN B 89 GLN B 99 ASN B 174 ASN ** Y 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN K 42 ASN O 70 GLN L 39 ASN L 50 ASN ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.071 64089 Z= 0.416 Angle : 0.982 26.669 93144 Z= 0.503 Chirality : 0.049 0.279 11496 Planarity : 0.009 0.146 6769 Dihedral : 16.132 179.159 20621 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.85 % Favored : 94.05 % Rotamer Outliers : 4.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 3849 helix: -0.73 (0.14), residues: 1243 sheet: -0.16 (0.20), residues: 669 loop : -1.41 (0.13), residues: 1937 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 553 time to evaluate : 3.589 Fit side-chains outliers start: 150 outliers final: 80 residues processed: 643 average time/residue: 1.5535 time to fit residues: 1270.4763 Evaluate side-chains 615 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 535 time to evaluate : 3.499 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 57 residues processed: 25 average time/residue: 0.7487 time to fit residues: 33.2796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 168 optimal weight: 3.9990 chunk 450 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 293 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 501 optimal weight: 8.9990 chunk 416 optimal weight: 8.9990 chunk 232 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 263 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 145 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 HIS D 110 ASN B 99 ASN B 174 ASN ** Y 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 117 GLN P 79 HIS ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN O 70 GLN L 39 ASN L 50 ASN ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 64089 Z= 0.234 Angle : 0.821 24.303 93144 Z= 0.434 Chirality : 0.042 0.262 11496 Planarity : 0.008 0.136 6769 Dihedral : 15.824 179.782 20621 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.81 % Favored : 95.12 % Rotamer Outliers : 4.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3849 helix: -0.44 (0.14), residues: 1238 sheet: -0.14 (0.20), residues: 669 loop : -1.31 (0.13), residues: 1942 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 543 time to evaluate : 3.527 Fit side-chains outliers start: 135 outliers final: 90 residues processed: 633 average time/residue: 1.5685 time to fit residues: 1267.6472 Evaluate side-chains 626 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 536 time to evaluate : 3.539 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 68 residues processed: 25 average time/residue: 0.6479 time to fit residues: 31.0070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 483 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 285 optimal weight: 0.0870 chunk 365 optimal weight: 8.9990 chunk 283 optimal weight: 3.9990 chunk 421 optimal weight: 8.9990 chunk 279 optimal weight: 2.9990 chunk 499 optimal weight: 0.9990 chunk 312 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 145 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS B 99 ASN B 174 ASN ** Y 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN K 47 ASN O 70 GLN E 66 GLN L 39 ASN ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 64089 Z= 0.196 Angle : 0.777 23.538 93144 Z= 0.414 Chirality : 0.040 0.299 11496 Planarity : 0.007 0.132 6769 Dihedral : 15.642 179.924 20621 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.01 % Favored : 94.91 % Rotamer Outliers : 3.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 3849 helix: -0.23 (0.15), residues: 1241 sheet: -0.06 (0.20), residues: 664 loop : -1.24 (0.13), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 543 time to evaluate : 4.055 Fit side-chains outliers start: 126 outliers final: 82 residues processed: 635 average time/residue: 1.5392 time to fit residues: 1247.1074 Evaluate side-chains 614 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 532 time to evaluate : 3.463 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 70 residues processed: 14 average time/residue: 0.7754 time to fit residues: 20.8595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 308 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 317 optimal weight: 2.9990 chunk 340 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 392 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 145 GLN J 112 GLN C 76 ASN B 99 ASN B 174 ASN ** Y 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 117 GLN P 79 HIS ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN K 47 ASN O 70 GLN E 66 GLN L 39 ASN ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 64089 Z= 0.213 Angle : 0.792 24.064 93144 Z= 0.420 Chirality : 0.041 0.326 11496 Planarity : 0.007 0.135 6769 Dihedral : 15.635 179.818 20621 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.88 % Favored : 95.04 % Rotamer Outliers : 3.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 3849 helix: -0.19 (0.15), residues: 1239 sheet: -0.04 (0.20), residues: 671 loop : -1.23 (0.13), residues: 1939 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 523 time to evaluate : 3.718 Fit side-chains outliers start: 127 outliers final: 93 residues processed: 615 average time/residue: 1.5788 time to fit residues: 1238.8488 Evaluate side-chains 612 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 519 time to evaluate : 3.491 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 78 residues processed: 18 average time/residue: 0.5726 time to fit residues: 22.0817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 454 optimal weight: 7.9990 chunk 478 optimal weight: 0.4980 chunk 436 optimal weight: 10.0000 chunk 465 optimal weight: 3.9990 chunk 280 optimal weight: 7.9990 chunk 202 optimal weight: 8.9990 chunk 365 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 420 optimal weight: 9.9990 chunk 440 optimal weight: 10.0000 chunk 463 optimal weight: 0.0030 overall best weight: 4.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 145 GLN J 112 GLN C 76 ASN B 99 ASN B 173 HIS B 174 ASN ** Y 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 117 GLN P 79 HIS ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN O 70 GLN E 66 GLN L 39 ASN ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 64089 Z= 0.355 Angle : 0.925 26.434 93144 Z= 0.479 Chirality : 0.047 0.410 11496 Planarity : 0.009 0.144 6769 Dihedral : 15.973 179.543 20621 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.92 % Favored : 93.97 % Rotamer Outliers : 3.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 3849 helix: -0.53 (0.14), residues: 1237 sheet: -0.11 (0.20), residues: 663 loop : -1.41 (0.13), residues: 1949 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 534 time to evaluate : 3.619 Fit side-chains outliers start: 129 outliers final: 90 residues processed: 625 average time/residue: 1.5707 time to fit residues: 1250.6663 Evaluate side-chains 612 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 522 time to evaluate : 3.515 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 72 residues processed: 19 average time/residue: 0.5514 time to fit residues: 22.6708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 305 optimal weight: 2.9990 chunk 491 optimal weight: 3.9990 chunk 300 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 342 optimal weight: 6.9990 chunk 516 optimal weight: 10.0000 chunk 474 optimal weight: 4.9990 chunk 410 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 317 optimal weight: 7.9990 chunk 251 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 145 GLN J 112 GLN B 99 ASN B 173 HIS B 174 ASN ** Y 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 117 GLN P 79 HIS ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN O 70 GLN L 39 ASN ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 64089 Z= 0.378 Angle : 0.955 26.370 93144 Z= 0.493 Chirality : 0.049 0.520 11496 Planarity : 0.009 0.144 6769 Dihedral : 16.102 179.394 20621 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.03 % Favored : 93.87 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 3849 helix: -0.72 (0.14), residues: 1234 sheet: -0.28 (0.20), residues: 678 loop : -1.49 (0.13), residues: 1937 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 528 time to evaluate : 3.526 Fit side-chains outliers start: 116 outliers final: 85 residues processed: 619 average time/residue: 1.5728 time to fit residues: 1239.0477 Evaluate side-chains 606 residues out of total 3414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 521 time to evaluate : 3.476 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 77 residues processed: 10 average time/residue: 0.6791 time to fit residues: 15.2289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 326 optimal weight: 10.0000 chunk 437 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 378 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 411 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 422 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 75 optimal weight: 0.0770 overall best weight: 1.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 145 GLN J 112 GLN D 110 ASN B 99 ASN B 173 HIS B 174 ASN ** Y 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN c 24 GLN O 70 GLN L 39 ASN ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.149724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.140550 restraints weight = 64586.647| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 0.19 r_work: 0.3370 rms_B_bonded: 0.74 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 1.60 restraints_weight: 0.2500 r_work: 0.3249 rms_B_bonded: 2.51 restraints_weight: 0.1250 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 64089 Z= 0.197 Angle : 0.795 23.600 93144 Z= 0.423 Chirality : 0.041 0.480 11496 Planarity : 0.007 0.133 6769 Dihedral : 15.716 179.993 20621 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 3849 helix: -0.30 (0.15), residues: 1241 sheet: -0.12 (0.20), residues: 667 loop : -1.29 (0.13), residues: 1941 =============================================================================== Job complete usr+sys time: 17794.34 seconds wall clock time: 310 minutes 44.21 seconds (18644.21 seconds total)