Starting phenix.real_space_refine on Sat Dec 16 13:28:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vof_21262/12_2023/6vof_21262_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vof_21262/12_2023/6vof_21262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vof_21262/12_2023/6vof_21262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vof_21262/12_2023/6vof_21262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vof_21262/12_2023/6vof_21262_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vof_21262/12_2023/6vof_21262_updated.pdb" } resolution = 4.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 98 5.16 5 C 21813 2.51 5 N 6336 2.21 5 O 6921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 37": "OD1" <-> "OD2" Residue "A GLU 47": "OE1" <-> "OE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 263": "OD1" <-> "OD2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "D ASP 366": "OD1" <-> "OD2" Residue "D ASP 403": "OD1" <-> "OD2" Residue "D GLU 416": "OE1" <-> "OE2" Residue "D PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "E ASP 211": "OD1" <-> "OD2" Residue "E TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 347": "OD1" <-> "OD2" Residue "E ASP 369": "OD1" <-> "OD2" Residue "E TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 403": "OD1" <-> "OD2" Residue "E PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 32": "OD1" <-> "OD2" Residue "F PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 125": "OD1" <-> "OD2" Residue "F PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 273": "OD1" <-> "OD2" Residue "F ASP 336": "OD1" <-> "OD2" Residue "F ASP 347": "OD1" <-> "OD2" Residue "F ASP 369": "OD1" <-> "OD2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 130": "OD1" <-> "OD2" Residue "d GLU 160": "OE1" <-> "OE2" Residue "d TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 49": "OD1" <-> "OD2" Residue "g PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 126": "OD1" <-> "OD2" Residue "g TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 267": "OE1" <-> "OE2" Residue "g GLU 332": "OE1" <-> "OE2" Residue "e ASP 80": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35182 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3796 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3832 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3829 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 481} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3589 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 451} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3600 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3610 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1360 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 173} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2444 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 308} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "e" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 926 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "I" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 746 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'TRANS': 150} Unresolved non-hydrogen bonds: 486 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 385 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 16, 'ASP:plan': 4, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 287 Chain: "J" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 681 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 3, 'TRANS': 132} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 396 Unresolved non-hydrogen angles: 491 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 15, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "a" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1082 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 185} Link IDs: {'PTRANS': 14, 'TRANS': 205} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 691 Unresolved non-hydrogen angles: 912 Unresolved non-hydrogen dihedrals: 583 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 6, 'TRP:plan': 5, 'HIS:plan': 3, 'PHE:plan': 17, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 340 Chain: "M" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 403 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "N" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 396 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "O" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 390 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "P" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 392 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "Q" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 393 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "R" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 392 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "S" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 396 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "T" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 402 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "U" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 400 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "V" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 392 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "W" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 406 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "X" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 402 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "Y" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 386 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "Z" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 386 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.91, per 1000 atoms: 0.54 Number of scatterers: 35182 At special positions: 0 Unit cell: (130, 203.84, 169.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 P 14 15.00 O 6921 8.00 N 6336 7.00 C 21813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.40 Conformation dependent library (CDL) restraints added in 7.9 seconds 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9402 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 167 helices and 31 sheets defined 55.3% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.42 Creating SS restraints... Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 176 through 189 removed outlier: 4.165A pdb=" N GLN A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLY A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 233 through 252 Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 289 through 300 removed outlier: 3.962A pdb=" N PHE A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 374 through 394 removed outlier: 4.230A pdb=" N LEU A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 5.477A pdb=" N GLN A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 445 through 448 removed outlier: 3.790A pdb=" N SER A 448 " --> pdb=" O TYR A 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 448' Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.984A pdb=" N ARG A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 484 through 500 removed outlier: 3.526A pdb=" N GLN A 495 " --> pdb=" O LYS A 491 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 19 Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 233 through 252 Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 291 through 299 Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 348 through 351 No H-bonds generated for 'chain 'B' and resid 348 through 351' Processing helix chain 'B' and resid 368 through 371 Processing helix chain 'B' and resid 374 through 397 removed outlier: 4.428A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 421 Processing helix chain 'B' and resid 431 through 442 Processing helix chain 'B' and resid 453 through 468 Processing helix chain 'B' and resid 470 through 479 Processing helix chain 'B' and resid 484 through 501 removed outlier: 3.877A pdb=" N GLN B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 17 Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 233 through 251 Proline residue: C 240 - end of helix removed outlier: 3.599A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 277 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 289 through 301 removed outlier: 3.673A pdb=" N PHE C 292 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS C 295 " --> pdb=" O PHE C 292 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU C 300 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 325 No H-bonds generated for 'chain 'C' and resid 323 through 325' Processing helix chain 'C' and resid 331 through 337 removed outlier: 4.254A pdb=" N ILE C 336 " --> pdb=" O PRO C 332 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER C 337 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 368 through 371 Processing helix chain 'C' and resid 374 through 380 Processing helix chain 'C' and resid 383 through 398 removed outlier: 3.595A pdb=" N GLN C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 420 Processing helix chain 'C' and resid 431 through 442 Processing helix chain 'C' and resid 454 through 468 Processing helix chain 'C' and resid 470 through 479 removed outlier: 3.592A pdb=" N GLU C 474 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 502 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 178 through 192 Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 243 through 262 removed outlier: 5.352A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 289 Processing helix chain 'D' and resid 302 through 312 removed outlier: 4.118A pdb=" N ARG D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 382 through 408 removed outlier: 4.370A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA D 406 " --> pdb=" O GLN D 402 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 430 Processing helix chain 'D' and resid 451 through 463 Processing helix chain 'D' and resid 471 through 473 No H-bonds generated for 'chain 'D' and resid 471 through 473' Processing helix chain 'D' and resid 480 through 494 Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 243 through 262 removed outlier: 4.081A pdb=" N ARG E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 288 removed outlier: 3.719A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 312 Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 354 through 358 Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 384 through 408 removed outlier: 5.161A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 431 removed outlier: 4.643A pdb=" N THR E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E 422 " --> pdb=" O ARG E 418 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 442 Processing helix chain 'E' and resid 451 through 461 Processing helix chain 'E' and resid 466 through 468 No H-bonds generated for 'chain 'E' and resid 466 through 468' Processing helix chain 'E' and resid 471 through 474 Processing helix chain 'E' and resid 480 through 495 Processing helix chain 'F' and resid 103 through 106 Processing helix chain 'F' and resid 154 through 159 Processing helix chain 'F' and resid 178 through 189 Processing helix chain 'F' and resid 206 through 219 Processing helix chain 'F' and resid 243 through 262 removed outlier: 4.669A pdb=" N GLY F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU F 251 " --> pdb=" O MET F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 289 removed outlier: 3.581A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 311 Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 337 through 345 removed outlier: 3.813A pdb=" N THR F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 382 through 405 removed outlier: 4.054A pdb=" N THR F 394 " --> pdb=" O ARG F 390 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 431 Processing helix chain 'F' and resid 438 through 440 No H-bonds generated for 'chain 'F' and resid 438 through 440' Processing helix chain 'F' and resid 451 through 463 removed outlier: 4.471A pdb=" N PHE F 458 " --> pdb=" O THR F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 474 removed outlier: 3.863A pdb=" N PHE F 474 " --> pdb=" O GLU F 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 471 through 474' Processing helix chain 'F' and resid 480 through 492 Processing helix chain 'd' and resid 74 through 89 Processing helix chain 'd' and resid 92 through 106 Processing helix chain 'd' and resid 109 through 116 Processing helix chain 'd' and resid 122 through 136 Processing helix chain 'd' and resid 140 through 151 Processing helix chain 'd' and resid 154 through 172 removed outlier: 3.640A pdb=" N VAL d 158 " --> pdb=" O ILE d 155 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LYS d 159 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU d 162 " --> pdb=" O LYS d 159 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN d 163 " --> pdb=" O GLU d 160 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU d 166 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 202 Processing helix chain 'd' and resid 238 through 248 removed outlier: 4.193A pdb=" N LEU d 248 " --> pdb=" O ILE d 244 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 99 Proline residue: g 84 - end of helix Processing helix chain 'g' and resid 133 through 151 removed outlier: 4.841A pdb=" N LEU g 138 " --> pdb=" O ASN g 134 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 162 through 169 Processing helix chain 'g' and resid 188 through 203 removed outlier: 4.459A pdb=" N ILE g 194 " --> pdb=" O GLU g 190 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP g 197 " --> pdb=" O ALA g 193 " (cutoff:3.500A) Processing helix chain 'g' and resid 291 through 361 Proline residue: g 297 - end of helix removed outlier: 4.246A pdb=" N ASP g 328 " --> pdb=" O SER g 324 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 103 removed outlier: 4.669A pdb=" N GLU e 100 " --> pdb=" O LEU e 96 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 130 removed outlier: 4.110A pdb=" N ASN e 130 " --> pdb=" O VAL e 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 157 Processing helix chain 'I' and resid 163 through 181 Processing helix chain 'J' and resid 88 through 201 removed outlier: 4.005A pdb=" N THR J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Proline residue: J 111 - end of helix Processing helix chain 'J' and resid 205 through 218 Processing helix chain 'a' and resid 38 through 58 Processing helix chain 'a' and resid 69 through 86 Processing helix chain 'a' and resid 95 through 113 Processing helix chain 'a' and resid 130 through 132 No H-bonds generated for 'chain 'a' and resid 130 through 132' Processing helix chain 'a' and resid 134 through 154 Processing helix chain 'a' and resid 172 through 207 Proline residue: a 183 - end of helix removed outlier: 4.158A pdb=" N LEU a 190 " --> pdb=" O LEU a 186 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 243 Proline residue: a 215 - end of helix removed outlier: 4.099A pdb=" N SER a 224 " --> pdb=" O LEU a 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 41 removed outlier: 4.532A pdb=" N SER M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE M 22 " --> pdb=" O GLY M 18 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLY M 23 " --> pdb=" O LEU M 19 " (cutoff:3.500A) Proline residue: M 24 - end of helix removed outlier: 3.946A pdb=" N GLY M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 76 removed outlier: 3.523A pdb=" N ARG M 50 " --> pdb=" O GLU M 46 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER M 56 " --> pdb=" O THR M 52 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU M 63 " --> pdb=" O PHE M 59 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR M 64 " --> pdb=" O MET M 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.403A pdb=" N SER N 21 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE N 22 " --> pdb=" O GLY N 18 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY N 23 " --> pdb=" O LEU N 19 " (cutoff:3.500A) Proline residue: N 24 - end of helix Processing helix chain 'N' and resid 47 through 75 Processing helix chain 'O' and resid 5 through 21 removed outlier: 3.944A pdb=" N SER O 21 " --> pdb=" O VAL O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 41 Processing helix chain 'O' and resid 43 through 75 removed outlier: 4.752A pdb=" N GLY O 47 " --> pdb=" O GLU O 44 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA O 58 " --> pdb=" O LEU O 55 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA O 62 " --> pdb=" O PHE O 59 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU O 63 " --> pdb=" O MET O 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 41 Proline residue: P 24 - end of helix removed outlier: 3.979A pdb=" N GLY P 38 " --> pdb=" O GLN P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 74 removed outlier: 3.855A pdb=" N GLU P 46 " --> pdb=" O PRO P 43 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLY P 47 " --> pdb=" O GLU P 44 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU P 54 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 Proline residue: Q 24 - end of helix Processing helix chain 'Q' and resid 43 through 75 removed outlier: 4.814A pdb=" N GLY Q 47 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS Q 48 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU Q 61 " --> pdb=" O ALA Q 58 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA Q 73 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 41 removed outlier: 3.535A pdb=" N GLY R 14 " --> pdb=" O VAL R 10 " (cutoff:3.500A) Proline residue: R 24 - end of helix Processing helix chain 'R' and resid 44 through 75 removed outlier: 4.468A pdb=" N GLY R 47 " --> pdb=" O GLU R 44 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE R 49 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU R 53 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU R 61 " --> pdb=" O ALA R 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 41 removed outlier: 3.747A pdb=" N GLY S 14 " --> pdb=" O VAL S 10 " (cutoff:3.500A) Proline residue: S 24 - end of helix Processing helix chain 'S' and resid 46 through 75 Processing helix chain 'T' and resid 4 through 41 removed outlier: 3.651A pdb=" N GLY T 14 " --> pdb=" O VAL T 10 " (cutoff:3.500A) Proline residue: T 24 - end of helix Processing helix chain 'T' and resid 43 through 75 removed outlier: 5.564A pdb=" N GLY T 47 " --> pdb=" O GLU T 44 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU T 61 " --> pdb=" O ALA T 58 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU T 68 " --> pdb=" O ILE T 65 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU T 75 " --> pdb=" O LEU T 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 41 removed outlier: 3.624A pdb=" N SER U 21 " --> pdb=" O VAL U 17 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE U 22 " --> pdb=" O GLY U 18 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLY U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) Proline residue: U 24 - end of helix removed outlier: 4.892A pdb=" N GLY U 29 " --> pdb=" O GLY U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 75 removed outlier: 4.173A pdb=" N PHE U 59 " --> pdb=" O LEU U 55 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU U 63 " --> pdb=" O PHE U 59 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR U 64 " --> pdb=" O MET U 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 41 removed outlier: 3.543A pdb=" N SER V 21 " --> pdb=" O VAL V 17 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE V 22 " --> pdb=" O GLY V 18 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY V 23 " --> pdb=" O LEU V 19 " (cutoff:3.500A) Proline residue: V 24 - end of helix removed outlier: 3.805A pdb=" N GLY V 29 " --> pdb=" O GLY V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 76 removed outlier: 5.555A pdb=" N GLY V 47 " --> pdb=" O GLU V 44 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE V 49 " --> pdb=" O GLU V 46 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA V 62 " --> pdb=" O PHE V 59 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU V 63 " --> pdb=" O MET V 60 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE V 76 " --> pdb=" O ALA V 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 41 removed outlier: 4.134A pdb=" N VAL W 17 " --> pdb=" O ALA W 13 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER W 21 " --> pdb=" O VAL W 17 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE W 22 " --> pdb=" O GLY W 18 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY W 23 " --> pdb=" O LEU W 19 " (cutoff:3.500A) Proline residue: W 24 - end of helix removed outlier: 4.069A pdb=" N GLY W 29 " --> pdb=" O GLY W 25 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY W 38 " --> pdb=" O GLN W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 76 removed outlier: 5.233A pdb=" N GLY W 47 " --> pdb=" O GLU W 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU W 53 " --> pdb=" O ARG W 50 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU W 54 " --> pdb=" O GLY W 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA W 62 " --> pdb=" O PHE W 59 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU W 63 " --> pdb=" O MET W 60 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR W 66 " --> pdb=" O LEU W 63 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE W 76 " --> pdb=" O ALA W 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 41 removed outlier: 4.104A pdb=" N VAL X 17 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER X 21 " --> pdb=" O VAL X 17 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE X 22 " --> pdb=" O GLY X 18 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLY X 23 " --> pdb=" O LEU X 19 " (cutoff:3.500A) Proline residue: X 24 - end of helix removed outlier: 4.217A pdb=" N GLY X 29 " --> pdb=" O GLY X 25 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY X 38 " --> pdb=" O GLN X 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 75 removed outlier: 4.303A pdb=" N GLY X 47 " --> pdb=" O GLU X 44 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR X 52 " --> pdb=" O ILE X 49 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU X 63 " --> pdb=" O MET X 60 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU X 68 " --> pdb=" O ILE X 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 19 removed outlier: 3.516A pdb=" N VAL Y 17 " --> pdb=" O ALA Y 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 21 through 41 removed outlier: 3.547A pdb=" N GLY Y 29 " --> pdb=" O GLY Y 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY Y 38 " --> pdb=" O GLN Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 76 removed outlier: 4.813A pdb=" N LEU Y 63 " --> pdb=" O PHE Y 59 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR Y 64 " --> pdb=" O MET Y 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 41 removed outlier: 4.084A pdb=" N VAL Z 17 " --> pdb=" O ALA Z 13 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER Z 21 " --> pdb=" O VAL Z 17 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE Z 22 " --> pdb=" O GLY Z 18 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) Proline residue: Z 24 - end of helix removed outlier: 3.938A pdb=" N GLY Z 29 " --> pdb=" O GLY Z 25 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY Z 38 " --> pdb=" O GLN Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 76 removed outlier: 3.843A pdb=" N ALA Z 62 " --> pdb=" O ALA Z 58 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU Z 63 " --> pdb=" O PHE Z 59 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY Z 67 " --> pdb=" O LEU Z 63 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.656A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N MET A 77 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLY A 62 " --> pdb=" O MET A 77 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.644A pdb=" N GLU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 168 through 170 removed outlier: 3.637A pdb=" N VAL A 320 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY A 170 " --> pdb=" O VAL A 320 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 225 through 227 removed outlier: 3.506A pdb=" N LEU A 258 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 72 through 75 Processing sheet with id= F, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.244A pdb=" N GLU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.545A pdb=" N VAL B 320 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 314 through 316 removed outlier: 7.038A pdb=" N THR B 257 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 193 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE B 260 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 195 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 225 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N GLY B 200 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N GLU B 227 " --> pdb=" O GLY B 200 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 29 through 31 Processing sheet with id= J, first strand: chain 'C' and resid 34 through 36 removed outlier: 3.544A pdb=" N ILE C 39 " --> pdb=" O GLY C 36 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.763A pdb=" N VAL C 100 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 167 through 170 Processing sheet with id= M, first strand: chain 'C' and resid 193 through 198 Processing sheet with id= N, first strand: chain 'C' and resid 64 through 67 removed outlier: 6.119A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 23 through 27 removed outlier: 6.511A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= Q, first strand: chain 'D' and resid 167 through 169 removed outlier: 8.046A pdb=" N ILE D 168 " --> pdb=" O ILE D 321 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N SER D 323 " --> pdb=" O ILE D 168 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 200 through 204 removed outlier: 7.394A pdb=" N VAL D 235 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLY D 203 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLY D 237 " --> pdb=" O GLY D 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 23 through 27 removed outlier: 6.419A pdb=" N ASP E 32 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE E 26 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN E 67 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL E 77 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL E 65 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= U, first strand: chain 'E' and resid 348 through 351 removed outlier: 6.614A pdb=" N SER E 323 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU E 170 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLN E 325 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLY E 172 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL E 327 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 199 through 204 Processing sheet with id= W, first strand: chain 'F' and resid 20 through 22 Processing sheet with id= X, first strand: chain 'F' and resid 23 through 27 removed outlier: 6.729A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL F 61 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= Z, first strand: chain 'F' and resid 348 through 350 removed outlier: 6.488A pdb=" N SER F 323 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU F 170 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN F 325 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 200 through 204 removed outlier: 7.421A pdb=" N VAL F 235 " --> pdb=" O GLY F 201 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLY F 203 " --> pdb=" O VAL F 235 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLY F 237 " --> pdb=" O GLY F 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'g' and resid 226 through 228 removed outlier: 3.642A pdb=" N VAL g 226 " --> pdb=" O TYR g 214 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR g 214 " --> pdb=" O VAL g 226 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR g 156 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL g 122 " --> pdb=" O THR g 156 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE g 158 " --> pdb=" O VAL g 122 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG g 178 " --> pdb=" O SER g 159 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'g' and resid 253 through 256 removed outlier: 3.629A pdb=" N LEU g 254 " --> pdb=" O ASP g 269 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP g 269 " --> pdb=" O LEU g 254 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'e' and resid 74 through 77 removed outlier: 3.557A pdb=" N VAL e 7 " --> pdb=" O TRP e 15 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TRP e 15 " --> pdb=" O VAL e 7 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N THR e 9 " --> pdb=" O SER e 13 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER e 13 " --> pdb=" O THR e 9 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'e' and resid 22 through 25 2152 hydrogen bonds defined for protein. 5628 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.40 Time building geometry restraints manager: 17.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10548 1.33 - 1.45: 5498 1.45 - 1.57: 19304 1.57 - 1.69: 23 1.69 - 1.81: 185 Bond restraints: 35558 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.73e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C4 ATP F 601 " pdb=" C5 ATP F 601 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.76e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.45e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.46e+01 ... (remaining 35553 not shown) Histogram of bond angle deviations from ideal: 98.27 - 106.02: 813 106.02 - 113.77: 20494 113.77 - 121.51: 18954 121.51 - 129.26: 8117 129.26 - 137.01: 59 Bond angle restraints: 48437 Sorted by residual: angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 115.96 23.91 1.00e+00 1.00e+00 5.72e+02 angle pdb=" PA ATP F 601 " pdb=" O3A ATP F 601 " pdb=" PB ATP F 601 " ideal model delta sigma weight residual 136.83 114.95 21.88 1.00e+00 1.00e+00 4.79e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 118.11 21.76 1.00e+00 1.00e+00 4.74e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 118.96 20.91 1.00e+00 1.00e+00 4.37e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 116.98 19.85 1.00e+00 1.00e+00 3.94e+02 ... (remaining 48432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 20219 24.18 - 48.36: 1132 48.36 - 72.54: 123 72.54 - 96.72: 41 96.72 - 120.90: 3 Dihedral angle restraints: 21518 sinusoidal: 6866 harmonic: 14652 Sorted by residual: dihedral pdb=" CA TYR D 362 " pdb=" C TYR D 362 " pdb=" N PRO D 363 " pdb=" CA PRO D 363 " ideal model delta harmonic sigma weight residual 180.00 119.49 60.51 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual 180.00 -122.15 -57.85 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -127.48 -52.52 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 21515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 5221 0.085 - 0.170: 602 0.170 - 0.255: 26 0.255 - 0.340: 7 0.340 - 0.425: 2 Chirality restraints: 5858 Sorted by residual: chirality pdb=" CB ILE B 331 " pdb=" CA ILE B 331 " pdb=" CG1 ILE B 331 " pdb=" CG2 ILE B 331 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CB ILE C 331 " pdb=" CA ILE C 331 " pdb=" CG1 ILE C 331 " pdb=" CG2 ILE C 331 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CG LEU C 421 " pdb=" CB LEU C 421 " pdb=" CD1 LEU C 421 " pdb=" CD2 LEU C 421 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 5855 not shown) Planarity restraints: 6483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 28 " 0.046 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO D 29 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 338 " 0.047 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO F 339 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 339 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 339 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 343 " 0.024 2.00e-02 2.50e+03 1.99e-02 6.92e+00 pdb=" CG PHE F 343 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE F 343 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE F 343 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 343 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 343 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE F 343 " 0.004 2.00e-02 2.50e+03 ... (remaining 6480 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2588 2.72 - 3.27: 40624 3.27 - 3.81: 66128 3.81 - 4.36: 74659 4.36 - 4.90: 120564 Nonbonded interactions: 304563 Sorted by model distance: nonbonded pdb=" OE1 GLN F 376 " pdb=" O2' ATP C 601 " model vdw 2.176 2.440 nonbonded pdb=" O ILE A 475 " pdb=" OG1 THR A 479 " model vdw 2.216 2.440 nonbonded pdb=" NZ LYS D 154 " pdb=" O PHE D 430 " model vdw 2.226 2.520 nonbonded pdb=" O VAL D 102 " pdb=" OG1 THR D 128 " model vdw 2.229 2.440 nonbonded pdb=" OG1 THR g 229 " pdb=" O CYS g 240 " model vdw 2.232 2.440 ... (remaining 304558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 23 or (resid 24 through 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 322 or (resid 323 thro \ ugh 324 and (name N or name CA or name C or name O or name CB )) or resid 325 th \ rough 398 or (resid 399 through 400 and (name N or name CA or name C or name O o \ r name CB )) or resid 401 through 471 or (resid 472 and (name N or name CA or na \ me C or name O or name CB )) or resid 473 through 503 or resid 601)) selection = (chain 'B' and (resid 8 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 393 or (resid 394 thro \ ugh 397 and (name N or name CA or name C or name O or name CB )) or resid 398 or \ (resid 399 through 400 and (name N or name CA or name C or name O or name CB )) \ or resid 401 through 432 or (resid 433 and (name N or name CA or name C or name \ O or name CB )) or resid 434 through 503 or resid 601)) selection = (chain 'C' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 23 or (resid 24 through 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 322 or (resid 323 through 324 and ( \ name N or name CA or name C or name O or name CB )) or resid 325 through 393 or \ (resid 394 through 397 and (name N or name CA or name C or name O or name CB )) \ or resid 398 through 432 or (resid 433 and (name N or name CA or name C or name \ O or name CB )) or resid 434 through 471 or (resid 472 and (name N or name CA or \ name C or name O or name CB )) or resid 473 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and (resid 19 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 58 or (resid 59 and ( \ name N or name CA or name C or name O or name CB )) or resid 60 through 115 or ( \ resid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 \ through 118 or (resid 119 and (name N or name CA or name C or name O or name CB \ )) or resid 120 through 260 or (resid 261 and (name N or name CA or name C or na \ me O or name CB )) or resid 262 through 310 or (resid 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 407 or (resid 408 and (n \ ame N or name CA or name C or name O or name CB )) or resid 409 through 416 or ( \ resid 417 and (name N or name CA or name C or name O or name CB )) or resid 418 \ through 494)) selection = (chain 'E' and (resid 19 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 78 or (resid 79 and (name N or nam \ e CA or name C or name O or name CB )) or resid 80 through 260 or (resid 261 and \ (name N or name CA or name C or name O or name CB )) or resid 262 through 331 o \ r (resid 332 through 333 and (name N or name CA or name C or name O or name CB ) \ ) or resid 334 through 407 or (resid 408 and (name N or name CA or name C or nam \ e O or name CB )) or resid 409 through 414 or (resid 415 and (name N or name CA \ or name C or name O or name CB )) or resid 416 through 446 or (resid 447 and (na \ me N or name CA or name C or name O or name CB )) or resid 448 through 464 or (r \ esid 465 and (name N or name CA or name C or name O or name CB )) or resid 466 t \ hrough 494)) selection = (chain 'F' and (resid 19 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 and \ (name N or name CA or name C or name O or name CB )) or resid 60 through 78 or \ (resid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 t \ hrough 115 or (resid 116 and (name N or name CA or name C or name O or name CB ) \ ) or resid 117 through 118 or (resid 119 and (name N or name CA or name C or nam \ e O or name CB )) or resid 120 through 310 or (resid 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 317 or (resid 318 and (na \ me N or name CA or name C or name O or name CB )) or resid 319 through 331 or (r \ esid 332 through 333 and (name N or name CA or name C or name O or name CB )) or \ resid 334 through 414 or (resid 415 and (name N or name CA or name C or name O \ or name CB )) or resid 416 or (resid 417 and (name N or name CA or name C or nam \ e O or name CB )) or resid 418 through 446 or (resid 447 and (name N or name CA \ or name C or name O or name CB )) or resid 448 through 464 or (resid 465 and (na \ me N or name CA or name C or name O or name CB )) or resid 466 through 494)) } ncs_group { reference = (chain 'M' and ((resid 3 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or (resid 47 through 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 81)) selection = (chain 'N' and ((resid 3 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 through 58 or (resid 59 through 66 and (name N or name \ CA or name C or name O or name CB )) or resid 67 through 81)) selection = (chain 'O' and (resid 3 through 47 or (resid 48 through 50 and (name N or name C \ A or name C or name O or name CB )) or resid 51 through 81)) selection = (chain 'P' and (resid 3 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 81)) selection = (chain 'Q' and (resid 3 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or (resid 47 through 66 and (name N or name CA or name \ C or name O or name CB )) or resid 67 through 81)) selection = (chain 'R' and (resid 3 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 81)) selection = (chain 'S' and (resid 3 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or (resid 47 through 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 81)) selection = (chain 'T' and (resid 3 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 or (resid 48 through 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 or (resid 52 through 66 and (n \ ame N or name CA or name C or name O or name CB )) or resid 67 through 81)) selection = (chain 'U' and (resid 3 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 or (resid 48 through 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 81)) selection = (chain 'V' and (resid 3 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or (resid 47 through 66 and (name N or name CA or name \ C or name O or name CB )) or resid 67 through 81)) selection = (chain 'W' and ((resid 3 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or (resid 47 through 50 and (name N or name CA or name \ C or name O or name CB )) or (resid 51 through 66 and (name N or name CA or nam \ e C or name O or name CB )) or resid 67 through 81)) selection = (chain 'X' and ((resid 3 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 through 47 or (resid 48 through 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 81)) selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.350 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: 3.440 Extract box with map and model: 8.090 Check model and map are aligned: 0.560 Set scattering table: 0.370 Process input model: 96.200 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 0.092 35558 Z= 0.463 Angle : 1.029 23.913 48437 Z= 0.632 Chirality : 0.053 0.425 5858 Planarity : 0.006 0.070 6483 Dihedral : 15.507 120.901 12113 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.32 % Favored : 91.63 % Rotamer: Outliers : 0.76 % Allowed : 14.74 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.10), residues: 5123 helix: -1.66 (0.08), residues: 2866 sheet: -3.77 (0.19), residues: 438 loop : -2.98 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP e 15 HIS 0.010 0.002 HIS E 193 PHE 0.045 0.003 PHE F 343 TYR 0.026 0.003 TYR A 439 ARG 0.016 0.001 ARG E 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 365 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 384 average time/residue: 0.5036 time to fit residues: 310.2716 Evaluate side-chains 248 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 237 time to evaluate : 4.064 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3062 time to fit residues: 11.7084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 422 optimal weight: 6.9990 chunk 378 optimal weight: 8.9990 chunk 210 optimal weight: 0.0970 chunk 129 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 391 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 291 optimal weight: 0.9980 chunk 454 optimal weight: 30.0000 overall best weight: 3.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN B 43 HIS B 110 ASN B 186 ASN B 256 HIS B 415 GLN B 423 GLN B 425 GLN B 468 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 148 GLN C 186 ASN C 334 ASN C 389 GLN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN C 495 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 193 HIS D 299 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 GLN E 42 ASN E 133 HIS ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN F 141 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 489 ASN d 141 HIS g 76 GLN ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 228 HIS g 286 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 331 ASN ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 30 GLN e 36 ASN e 93 GLN e 116 ASN e 130 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35558 Z= 0.305 Angle : 0.708 11.771 48437 Z= 0.378 Chirality : 0.044 0.292 5858 Planarity : 0.006 0.090 6483 Dihedral : 7.963 116.439 5607 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.85 % Favored : 92.09 % Rotamer: Outliers : 0.34 % Allowed : 7.73 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.10 % 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: -2.06 (0.11), residues: 5123 helix: -0.25 (0.09), residues: 2875 sheet: -3.52 (0.20), residues: 444 loop : -2.53 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP e 15 HIS 0.007 0.002 HIS E 193 PHE 0.030 0.002 PHE F 343 TYR 0.040 0.002 TYR E 298 ARG 0.010 0.001 ARG E 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 316 time to evaluate : 4.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 326 average time/residue: 0.4599 time to fit residues: 253.6446 Evaluate side-chains 231 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 227 time to evaluate : 3.777 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3134 time to fit residues: 7.3712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 252 optimal weight: 0.0170 chunk 140 optimal weight: 0.7980 chunk 377 optimal weight: 7.9990 chunk 309 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 454 optimal weight: 40.0000 chunk 491 optimal weight: 8.9990 chunk 405 optimal weight: 40.0000 chunk 451 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 364 optimal weight: 6.9990 overall best weight: 1.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 423 GLN B 497 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 410 GLN C 423 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 GLN ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 228 HIS ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 342 ASN e 36 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 35558 Z= 0.213 Angle : 0.639 11.224 48437 Z= 0.334 Chirality : 0.043 0.288 5858 Planarity : 0.005 0.079 6483 Dihedral : 7.562 116.846 5607 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.11 % Favored : 92.88 % Rotamer: Outliers : 0.07 % Allowed : 5.98 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % 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: -1.39 (0.11), residues: 5123 helix: 0.32 (0.09), residues: 2859 sheet: -3.42 (0.21), residues: 420 loop : -2.24 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP e 15 HIS 0.007 0.001 HIS C 256 PHE 0.034 0.002 PHE F 343 TYR 0.028 0.002 TYR E 298 ARG 0.015 0.001 ARG C 165 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 319 time to evaluate : 4.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 321 average time/residue: 0.4624 time to fit residues: 248.8927 Evaluate side-chains 239 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 4.073 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3772 time to fit residues: 5.8761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 449 optimal weight: 5.9990 chunk 341 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 305 optimal weight: 9.9990 chunk 456 optimal weight: 10.0000 chunk 483 optimal weight: 0.0980 chunk 238 optimal weight: 0.4980 chunk 432 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 GLN E 325 GLN ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 36 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35558 Z= 0.237 Angle : 0.642 9.730 48437 Z= 0.337 Chirality : 0.043 0.263 5858 Planarity : 0.005 0.060 6483 Dihedral : 7.358 114.987 5607 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 23.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.63 % Favored : 92.35 % Rotamer: Outliers : 0.07 % Allowed : 5.50 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % 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: -1.02 (0.12), residues: 5123 helix: 0.64 (0.09), residues: 2862 sheet: -3.28 (0.21), residues: 430 loop : -2.11 (0.15), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP e 15 HIS 0.010 0.001 HIS B 295 PHE 0.028 0.002 PHE F 343 TYR 0.027 0.002 TYR E 162 ARG 0.023 0.001 ARG d 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 294 time to evaluate : 4.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 296 average time/residue: 0.4363 time to fit residues: 220.6832 Evaluate side-chains 223 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 4.014 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 402 optimal weight: 50.0000 chunk 274 optimal weight: 8.9990 chunk 7 optimal weight: 0.2980 chunk 359 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 412 optimal weight: 20.0000 chunk 334 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 433 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 GLN ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 346 GLN e 36 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35558 Z= 0.289 Angle : 0.667 10.018 48437 Z= 0.352 Chirality : 0.044 0.264 5858 Planarity : 0.005 0.066 6483 Dihedral : 7.389 113.284 5607 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 24.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.32 % Favored : 91.67 % Rotamer: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.12), residues: 5123 helix: 0.82 (0.10), residues: 2852 sheet: -3.20 (0.21), residues: 440 loop : -2.03 (0.15), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP e 15 HIS 0.007 0.001 HIS E 193 PHE 0.030 0.002 PHE F 343 TYR 0.035 0.002 TYR E 162 ARG 0.009 0.001 ARG g 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 4.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.4585 time to fit residues: 218.1571 Evaluate side-chains 216 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 4.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 162 optimal weight: 8.9990 chunk 435 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 283 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 483 optimal weight: 5.9990 chunk 401 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 160 optimal weight: 0.7980 chunk 253 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 GLN ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 36 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35558 Z= 0.292 Angle : 0.668 9.273 48437 Z= 0.352 Chirality : 0.044 0.276 5858 Planarity : 0.005 0.073 6483 Dihedral : 7.433 112.382 5607 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.33 % Favored : 91.65 % Rotamer: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.12), residues: 5123 helix: 0.91 (0.10), residues: 2854 sheet: -3.16 (0.22), residues: 425 loop : -1.97 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP e 15 HIS 0.007 0.001 HIS E 193 PHE 0.031 0.002 PHE F 474 TYR 0.025 0.002 TYR E 162 ARG 0.011 0.001 ARG E 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 4.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.4749 time to fit residues: 225.0690 Evaluate side-chains 219 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 4.245 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 466 optimal weight: 50.0000 chunk 54 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 353 optimal weight: 20.0000 chunk 273 optimal weight: 0.9980 chunk 407 optimal weight: 5.9990 chunk 270 optimal weight: 7.9990 chunk 481 optimal weight: 8.9990 chunk 301 optimal weight: 8.9990 chunk 293 optimal weight: 0.4980 chunk 222 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35558 Z= 0.189 Angle : 0.634 11.130 48437 Z= 0.326 Chirality : 0.043 0.287 5858 Planarity : 0.004 0.069 6483 Dihedral : 7.172 111.696 5607 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.83 % Favored : 93.15 % Rotamer: Outliers : 0.03 % Allowed : 2.27 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.12), residues: 5123 helix: 1.13 (0.10), residues: 2845 sheet: -3.03 (0.22), residues: 445 loop : -1.81 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP e 15 HIS 0.005 0.001 HIS B 295 PHE 0.032 0.002 PHE g 168 TYR 0.020 0.001 TYR E 298 ARG 0.006 0.000 ARG e 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 4.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 300 average time/residue: 0.4694 time to fit residues: 239.6869 Evaluate side-chains 221 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 3.821 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 298 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 287 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 306 optimal weight: 6.9990 chunk 328 optimal weight: 20.0000 chunk 238 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 378 optimal weight: 0.3980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 290 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35558 Z= 0.208 Angle : 0.636 10.243 48437 Z= 0.330 Chirality : 0.043 0.257 5858 Planarity : 0.004 0.053 6483 Dihedral : 7.045 109.421 5607 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.85 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.12), residues: 5123 helix: 1.25 (0.10), residues: 2841 sheet: -2.95 (0.22), residues: 442 loop : -1.72 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP e 15 HIS 0.003 0.001 HIS A 295 PHE 0.029 0.002 PHE F 343 TYR 0.057 0.001 TYR E 298 ARG 0.007 0.000 ARG e 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 3.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.3810 time to fit residues: 186.1016 Evaluate side-chains 226 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 3.014 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 438 optimal weight: 50.0000 chunk 461 optimal weight: 20.0000 chunk 421 optimal weight: 3.9990 chunk 449 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 352 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 405 optimal weight: 20.0000 chunk 424 optimal weight: 7.9990 chunk 447 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: