Starting phenix.real_space_refine (version: dev) on Tue Apr 5 08:35:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8i_10123/04_2022/6s8i_10123.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8i_10123/04_2022/6s8i_10123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8i_10123/04_2022/6s8i_10123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8i_10123/04_2022/6s8i_10123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8i_10123/04_2022/6s8i_10123.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8i_10123/04_2022/6s8i_10123.pdb" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.171 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "L TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 100": "OD1" <-> "OD2" Residue "L PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B ASP 607": "OD1" <-> "OD2" Residue "D GLU 523": "OE1" <-> "OE2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D ASP 607": "OD1" <-> "OD2" Residue "F GLU 523": "OE1" <-> "OE2" Residue "F ARG 559": "NH1" <-> "NH2" Residue "F ASP 607": "OD1" <-> "OD2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ASP 150": "OD1" <-> "OD2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 219": "NH1" <-> "NH2" Residue "E PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 100": "OD1" <-> "OD2" Residue "O PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 100": "OD1" <-> "OD2" Residue "U PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 92": "OD1" <-> "OD2" Residue "Y PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 92": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 12066 Number of models: 1 Model: "" Number of chains: 15 Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 814 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 109, 'PCIS': 1} Chain: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "D" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "F" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "C" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 814 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "U" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 814 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "P" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 109, 'PCIS': 1} Chain: "Y" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 109, 'PCIS': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.57, per 1000 atoms: 0.63 Number of scatterers: 12066 At special positions: 0 Unit cell: (101.88, 98.484, 123.105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 2295 8.00 N 2076 7.00 C 7644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=2.00 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.04 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.04 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.04 Simple disulfide: pdb=" SG CYS D 609 " - pdb=" SG CYS C 53 " distance=2.09 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.04 Simple disulfide: pdb=" SG CYS F 609 " - pdb=" SG CYS E 53 " distance=1.99 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 91 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 91 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 98 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 98 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 701 " - " NAG B 702 " " NAG D 701 " - " NAG D 702 " " NAG F 701 " - " NAG F 702 " NAG-ASN " NAG B 701 " - " ASN B 563 " " NAG D 701 " - " ASN D 563 " " NAG F 701 " - " ASN F 563 " Time building additional restraints: 5.04 Conformation dependent library (CDL) restraints added in 2.0 seconds 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2802 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 30 sheets defined 12.8% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.820A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.619A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 4.033A pdb=" N ILE B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.625A pdb=" N GLY B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 removed outlier: 3.602A pdb=" N ARG B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 4.034A pdb=" N ILE D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 3.625A pdb=" N GLY D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.602A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 4.033A pdb=" N ILE F 542 " --> pdb=" O ALA F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.626A pdb=" N GLY F 557 " --> pdb=" O GLY F 553 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.602A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.619A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 84 removed outlier: 3.619A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.820A pdb=" N GLU O 86 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 86 removed outlier: 3.820A pdb=" N GLU U 86 " --> pdb=" O ALA U 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.593A pdb=" N TRP L 38 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 5.893A pdb=" N GLY H 16 " --> pdb=" O SER H 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 60 through 62 removed outlier: 4.727A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 43 through 46 removed outlier: 4.666A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 43 through 46 removed outlier: 4.666A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA9, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AB1, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.753A pdb=" N GLU A 106 " --> pdb=" O CYS A 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 544 through 548 Processing sheet with id=AB3, first strand: chain 'D' and resid 580 through 581 removed outlier: 3.603A pdb=" N ASN C 98 " --> pdb=" O THR D 581 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 580 through 581 removed outlier: 3.603A pdb=" N ASN C 98 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 544 through 548 Processing sheet with id=AB6, first strand: chain 'F' and resid 580 through 581 removed outlier: 4.665A pdb=" N LEU E 35 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 580 through 581 Processing sheet with id=AB8, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB9, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.754A pdb=" N GLU C 106 " --> pdb=" O CYS C 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AC2, first strand: chain 'E' and resid 105 through 114 removed outlier: 6.753A pdb=" N GLU E 106 " --> pdb=" O CYS E 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.595A pdb=" N TRP O 38 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AC5, first strand: chain 'O' and resid 18 through 23 Processing sheet with id=AC6, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.593A pdb=" N TRP U 38 " --> pdb=" O LEU U 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 10 through 12 Processing sheet with id=AC8, first strand: chain 'U' and resid 18 through 23 Processing sheet with id=AC9, first strand: chain 'P' and resid 3 through 7 removed outlier: 5.893A pdb=" N GLY P 16 " --> pdb=" O SER P 87 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 60 through 62 removed outlier: 4.727A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Y' and resid 3 through 7 removed outlier: 5.892A pdb=" N GLY Y 16 " --> pdb=" O SER Y 87 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Y' and resid 60 through 62 removed outlier: 4.727A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1242 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: 3.96 Time building geometry restraints manager: 5.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3942 1.34 - 1.46: 2877 1.46 - 1.58: 5481 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 12360 Sorted by residual: bond pdb=" CG LEU Y 99 " pdb=" CD2 LEU Y 99 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CG LEU H 99 " pdb=" CD2 LEU H 99 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.14e+00 bond pdb=" CG LEU P 99 " pdb=" CD2 LEU P 99 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.11e+00 bond pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.39e+00 bond pdb=" CB CYS E 135 " pdb=" SG CYS E 135 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.39e+00 ... (remaining 12355 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.18: 458 107.18 - 113.90: 6548 113.90 - 120.62: 5000 120.62 - 127.34: 4645 127.34 - 134.06: 149 Bond angle restraints: 16800 Sorted by residual: angle pdb=" CA TYR U 52 " pdb=" CB TYR U 52 " pdb=" CG TYR U 52 " ideal model delta sigma weight residual 113.90 120.42 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" CA TYR O 52 " pdb=" CB TYR O 52 " pdb=" CG TYR O 52 " ideal model delta sigma weight residual 113.90 120.42 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" CA TRP H 107 " pdb=" CB TRP H 107 " pdb=" CG TRP H 107 " ideal model delta sigma weight residual 113.60 120.44 -6.84 1.90e+00 2.77e-01 1.30e+01 angle pdb=" CA TRP Y 107 " pdb=" CB TRP Y 107 " pdb=" CG TRP Y 107 " ideal model delta sigma weight residual 113.60 120.43 -6.83 1.90e+00 2.77e-01 1.29e+01 angle pdb=" CA TYR L 52 " pdb=" CB TYR L 52 " pdb=" CG TYR L 52 " ideal model delta sigma weight residual 113.90 120.37 -6.47 1.80e+00 3.09e-01 1.29e+01 ... (remaining 16795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 6535 17.07 - 34.13: 524 34.13 - 51.20: 165 51.20 - 68.27: 30 68.27 - 85.34: 12 Dihedral angle restraints: 7266 sinusoidal: 2841 harmonic: 4425 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 147 " pdb=" CB CYS C 147 " ideal model delta sinusoidal sigma weight residual -86.00 -13.01 -72.99 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS E 121 " pdb=" SG CYS E 121 " pdb=" SG CYS E 147 " pdb=" CB CYS E 147 " ideal model delta sinusoidal sigma weight residual -86.00 -13.03 -72.97 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS A 121 " pdb=" SG CYS A 121 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual -86.00 -13.04 -72.96 1 1.00e+01 1.00e-02 6.79e+01 ... (remaining 7263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 1815 0.193 - 0.387: 12 0.387 - 0.580: 3 0.580 - 0.774: 0 0.774 - 0.967: 3 Chirality restraints: 1833 Sorted by residual: chirality pdb=" C1 NAG B 702 " pdb=" O4 NAG B 701 " pdb=" C2 NAG B 702 " pdb=" O5 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.43 -0.97 2.00e-02 2.50e+03 2.34e+03 chirality pdb=" C1 NAG F 702 " pdb=" O4 NAG F 701 " pdb=" C2 NAG F 702 " pdb=" O5 NAG F 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.44 -0.96 2.00e-02 2.50e+03 2.33e+03 chirality pdb=" C1 NAG D 702 " pdb=" O4 NAG D 701 " pdb=" C2 NAG D 702 " pdb=" O5 NAG D 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.44 -0.96 2.00e-02 2.50e+03 2.32e+03 ... (remaining 1830 not shown) Planarity restraints: 2190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 563 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C ASN B 563 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN B 563 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU B 564 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 563 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C ASN F 563 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN F 563 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU F 564 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 70 " 0.018 2.00e-02 2.50e+03 1.49e-02 3.87e+00 pdb=" CG PHE H 70 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE H 70 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE H 70 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 70 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE H 70 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE H 70 " 0.003 2.00e-02 2.50e+03 ... (remaining 2187 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 644 2.72 - 3.26: 10988 3.26 - 3.81: 17663 3.81 - 4.35: 23182 4.35 - 4.90: 40220 Nonbonded interactions: 92697 Sorted by model distance: nonbonded pdb=" OG1 THR H 100 " pdb=" O ARG H 105 " model vdw 2.171 2.440 nonbonded pdb=" OG1 THR P 100 " pdb=" O ARG P 105 " model vdw 2.171 2.440 nonbonded pdb=" OG1 THR Y 100 " pdb=" O ARG Y 105 " model vdw 2.172 2.440 nonbonded pdb=" OD2 ASP L 100 " pdb=" OG1 THR A 144 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR A 99 " pdb=" O TYR A 162 " model vdw 2.276 2.440 ... (remaining 92692 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' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 7644 2.51 5 N 2076 2.21 5 O 2295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.710 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.120 Process input model: 35.570 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 0.059 12360 Z= 0.471 Angle : 0.948 7.482 16800 Z= 0.529 Chirality : 0.073 0.967 1833 Planarity : 0.006 0.042 2187 Dihedral : 14.034 85.336 4401 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 8.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1536 helix: -0.10 (0.40), residues: 144 sheet: 0.61 (0.20), residues: 573 loop : -0.69 (0.20), residues: 819 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 260 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 38 residues processed: 346 average time/residue: 0.9312 time to fit residues: 357.0058 Evaluate side-chains 206 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 1.385 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 32 residues processed: 6 average time/residue: 0.1248 time to fit residues: 3.2635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 40.0000 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 50.0000 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN L 82 GLN H 39 GLN A 39 HIS A 61 ASN A 107 ASN A 188 GLN B 516 HIS D 516 HIS ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS C 61 ASN C 107 ASN E 39 HIS E 61 ASN E 107 ASN O 40 GLN O 82 GLN U 40 GLN U 41 GLN U 82 GLN Y 39 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.068 12360 Z= 0.469 Angle : 0.808 8.301 16800 Z= 0.426 Chirality : 0.055 0.511 1833 Planarity : 0.006 0.041 2187 Dihedral : 5.442 19.697 1746 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 9.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1536 helix: 1.24 (0.47), residues: 126 sheet: 0.59 (0.20), residues: 579 loop : -0.79 (0.20), residues: 831 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 172 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 80 residues processed: 262 average time/residue: 0.9682 time to fit residues: 280.4793 Evaluate side-chains 247 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 167 time to evaluate : 1.330 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 63 residues processed: 17 average time/residue: 0.3230 time to fit residues: 8.7774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 0.0470 chunk 43 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN E 61 ASN Y 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 12360 Z= 0.203 Angle : 0.599 6.122 16800 Z= 0.319 Chirality : 0.049 0.571 1833 Planarity : 0.004 0.039 2187 Dihedral : 4.812 20.582 1746 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 7.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.20), residues: 1536 helix: 1.67 (0.48), residues: 126 sheet: 0.61 (0.21), residues: 576 loop : -0.70 (0.20), residues: 834 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 181 time to evaluate : 1.384 Fit side-chains revert: symmetry clash outliers start: 97 outliers final: 73 residues processed: 255 average time/residue: 0.9651 time to fit residues: 272.1869 Evaluate side-chains 236 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 163 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 56 residues processed: 17 average time/residue: 0.4863 time to fit residues: 11.7914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 30.0000 chunk 15 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN E 61 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.049 12360 Z= 0.464 Angle : 0.754 6.576 16800 Z= 0.396 Chirality : 0.052 0.502 1833 Planarity : 0.006 0.041 2187 Dihedral : 5.286 18.325 1746 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 8.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.20), residues: 1536 helix: 1.12 (0.50), residues: 126 sheet: 0.38 (0.20), residues: 594 loop : -1.06 (0.19), residues: 816 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 154 time to evaluate : 1.934 Fit side-chains outliers start: 104 outliers final: 86 residues processed: 230 average time/residue: 0.9863 time to fit residues: 251.7915 Evaluate side-chains 236 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 150 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 66 residues processed: 20 average time/residue: 0.4215 time to fit residues: 12.4207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 40.0000 chunk 126 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN A 61 ASN C 61 ASN C 228 ASN E 61 ASN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 12360 Z= 0.163 Angle : 0.563 6.478 16800 Z= 0.298 Chirality : 0.046 0.499 1833 Planarity : 0.004 0.040 2187 Dihedral : 4.605 18.545 1746 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 6.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1536 helix: 1.40 (0.49), residues: 126 sheet: 0.50 (0.20), residues: 570 loop : -0.89 (0.19), residues: 840 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 163 time to evaluate : 1.439 Fit side-chains outliers start: 85 outliers final: 70 residues processed: 225 average time/residue: 0.9692 time to fit residues: 242.6325 Evaluate side-chains 228 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 158 time to evaluate : 1.413 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 54 residues processed: 16 average time/residue: 0.2536 time to fit residues: 7.5639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 0.0170 chunk 142 optimal weight: 10.0000 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 61 ASN E 61 ASN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12360 Z= 0.174 Angle : 0.556 7.291 16800 Z= 0.292 Chirality : 0.045 0.434 1833 Planarity : 0.004 0.043 2187 Dihedral : 4.432 18.994 1746 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 6.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1536 helix: 1.58 (0.49), residues: 126 sheet: 0.46 (0.20), residues: 576 loop : -0.83 (0.20), residues: 834 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 162 time to evaluate : 1.452 Fit side-chains outliers start: 82 outliers final: 71 residues processed: 226 average time/residue: 0.9405 time to fit residues: 236.0055 Evaluate side-chains 228 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 157 time to evaluate : 1.421 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 58 residues processed: 13 average time/residue: 0.4672 time to fit residues: 9.2685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.3980 chunk 84 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 82 optimal weight: 0.3980 chunk 147 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 61 ASN E 61 ASN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 12360 Z= 0.131 Angle : 0.521 7.283 16800 Z= 0.272 Chirality : 0.044 0.404 1833 Planarity : 0.004 0.044 2187 Dihedral : 4.173 18.516 1746 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 5.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1536 helix: 1.75 (0.49), residues: 126 sheet: 0.56 (0.20), residues: 576 loop : -0.81 (0.20), residues: 834 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 166 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 59 residues processed: 229 average time/residue: 0.9064 time to fit residues: 231.6158 Evaluate side-chains 215 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 156 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 52 residues processed: 7 average time/residue: 0.2554 time to fit residues: 4.2104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 134 optimal weight: 0.0470 chunk 141 optimal weight: 1.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 61 ASN E 61 ASN O 41 GLN P 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 12360 Z= 0.231 Angle : 0.587 6.805 16800 Z= 0.305 Chirality : 0.046 0.430 1833 Planarity : 0.004 0.045 2187 Dihedral : 4.424 18.609 1746 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 5.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1536 helix: 1.62 (0.49), residues: 126 sheet: 0.56 (0.20), residues: 585 loop : -0.90 (0.20), residues: 825 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 149 time to evaluate : 1.455 Fit side-chains revert: symmetry clash outliers start: 73 outliers final: 66 residues processed: 210 average time/residue: 0.8892 time to fit residues: 208.7011 Evaluate side-chains 212 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 146 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 57 residues processed: 9 average time/residue: 0.1364 time to fit residues: 3.9676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 61 ASN E 61 ASN P 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 12360 Z= 0.157 Angle : 0.539 7.325 16800 Z= 0.280 Chirality : 0.044 0.413 1833 Planarity : 0.004 0.042 2187 Dihedral : 4.213 18.636 1746 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 5.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1536 helix: 1.69 (0.49), residues: 126 sheet: 0.52 (0.21), residues: 537 loop : -0.83 (0.19), residues: 873 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 154 time to evaluate : 1.396 Fit side-chains revert: symmetry clash outliers start: 65 outliers final: 62 residues processed: 209 average time/residue: 0.9096 time to fit residues: 213.2377 Evaluate side-chains 215 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 153 time to evaluate : 1.501 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 53 residues processed: 9 average time/residue: 0.2633 time to fit residues: 5.2638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 0.1980 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 121 optimal weight: 0.0030 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 61 ASN E 61 ASN P 39 GLN Y 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 12360 Z= 0.158 Angle : 0.538 7.180 16800 Z= 0.278 Chirality : 0.044 0.397 1833 Planarity : 0.004 0.041 2187 Dihedral : 4.124 18.526 1746 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 4.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1536 helix: 1.76 (0.49), residues: 126 sheet: 0.55 (0.21), residues: 549 loop : -0.80 (0.19), residues: 861 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 150 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 59 residues processed: 205 average time/residue: 0.9280 time to fit residues: 212.5093 Evaluate side-chains 206 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 147 time to evaluate : 1.480 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 53 residues processed: 6 average time/residue: 0.1483 time to fit residues: 3.3869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 61 ASN E 61 ASN P 39 GLN Y 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.181162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.143817 restraints weight = 13734.333| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.96 r_work: 0.3502 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work: 0.3458 rms_B_bonded: 2.75 restraints_weight: 0.1250 r_work: 0.3434 rms_B_bonded: 2.93 restraints_weight: 0.0625 r_work: 0.3405 rms_B_bonded: 3.23 restraints_weight: 0.0312 r_work: 0.3371 rms_B_bonded: 3.66 restraints_weight: 0.0156 r_work: 0.3329 rms_B_bonded: 4.27 restraints_weight: 0.0078 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12360 Z= 0.175 Angle : 0.549 7.220 16800 Z= 0.284 Chirality : 0.044 0.390 1833 Planarity : 0.004 0.041 2187 Dihedral : 4.168 18.521 1746 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 4.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1536 helix: 1.75 (0.49), residues: 126 sheet: 0.57 (0.21), residues: 549 loop : -0.80 (0.19), residues: 861 =============================================================================== Job complete usr+sys time: 4134.46 seconds wall clock time: 74 minutes 22.64 seconds (4462.64 seconds total)