Starting phenix.real_space_refine on Thu Feb 15 11:36:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8i_10123/02_2024/6s8i_10123.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8i_10123/02_2024/6s8i_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_10123/02_2024/6s8i_10123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8i_10123/02_2024/6s8i_10123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8i_10123/02_2024/6s8i_10123.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8i_10123/02_2024/6s8i_10123.pdb" } resolution = 2.99 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= 0.008 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 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. 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-5238/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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 109} 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 109} Chain: "Y" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 109} Chain: "G" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.85, per 1000 atoms: 0.57 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 G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG G 1 " - " ASN B 563 " " NAG I 1 " - " ASN D 563 " " NAG J 1 " - " ASN F 563 " Time building additional restraints: 4.50 Conformation dependent library (CDL) restraints added in 2.3 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: 1.44 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: 3.83 Time building geometry restraints manager: 4.92 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: 6607 17.07 - 34.13: 533 34.13 - 51.20: 174 51.20 - 68.27: 30 68.27 - 85.34: 12 Dihedral angle restraints: 7356 sinusoidal: 2931 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 7353 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 G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " 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 J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " 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 I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " 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 'G' selection = chain 'I' selection = chain 'J' } 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 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: 1.030 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: 0.000 Extract box with map and model: 4.140 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.890 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 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:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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= 0.475 Angle : 0.955 7.482 16800 Z= 0.530 Chirality : 0.073 0.967 1833 Planarity : 0.006 0.042 2187 Dihedral : 14.063 85.336 4491 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 8.13 % Allowed : 7.42 % Favored : 84.45 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.008 0.002 HIS U 37 PHE 0.034 0.003 PHE Y 70 TYR 0.027 0.003 TYR L 94 ARG 0.015 0.001 ARG A 54 *********************** 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 : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6622 (mt-10) REVERT: C 56 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7051 (tptt) REVERT: E 56 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6766 (tptt) REVERT: E 156 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8025 (mt-10) REVERT: P 6 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6867 (mt-10) REVERT: P 97 TYR cc_start: 0.8407 (m-80) cc_final: 0.8193 (m-80) REVERT: Y 53 SER cc_start: 0.7716 (t) cc_final: 0.7447 (p) outliers start: 102 outliers final: 38 residues processed: 346 average time/residue: 0.9874 time to fit residues: 375.3134 Evaluate side-chains 211 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 169 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain P residue 6 GLU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 107 TRP Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 60 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 107 TRP 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: 4.9990 chunk 72 optimal weight: 50.0000 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 C 39 HIS C 61 ASN C 107 ASN E 39 HIS E 61 ASN E 107 ASN O 40 GLN O 41 GLN O 82 GLN U 40 GLN U 41 GLN U 82 GLN P 39 GLN Y 39 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 12360 Z= 0.438 Angle : 0.797 7.846 16800 Z= 0.414 Chirality : 0.053 0.424 1833 Planarity : 0.006 0.042 2187 Dihedral : 8.426 56.025 1896 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 8.77 % Allowed : 14.99 % Favored : 76.24 % 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: 0.02 (0.20), residues: 1536 helix: 1.31 (0.48), residues: 126 sheet: 1.05 (0.22), residues: 501 loop : -0.81 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP P 107 HIS 0.007 0.002 HIS U 37 PHE 0.017 0.003 PHE H 70 TYR 0.024 0.003 TYR U 52 ARG 0.009 0.001 ARG B 596 *********************** 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 284 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 174 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6623 (mt-10) REVERT: H 43 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7488 (mptp) REVERT: A 140 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7343 (mtpp) REVERT: B 547 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8303 (tp) REVERT: C 112 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: C 219 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6633 (mtp180) REVERT: E 56 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.7035 (tptt) REVERT: E 140 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7342 (mtpp) REVERT: E 156 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8033 (mt-10) REVERT: P 6 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6837 (mt-10) outliers start: 110 outliers final: 72 residues processed: 257 average time/residue: 1.0662 time to fit residues: 300.5149 Evaluate side-chains 245 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 164 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain P residue 6 GLU Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 98 CYS Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 115 VAL Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 19 ARG Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 60 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 90 THR Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 0.0070 chunk 43 optimal weight: 0.4980 chunk 115 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.3002 ------------------------------------------------------------------------------- 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 ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12360 Z= 0.205 Angle : 0.602 5.567 16800 Z= 0.316 Chirality : 0.048 0.493 1833 Planarity : 0.005 0.038 2187 Dihedral : 7.097 57.877 1869 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.74 % Allowed : 17.86 % Favored : 76.40 % 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: 0.08 (0.20), residues: 1536 helix: 1.59 (0.49), residues: 126 sheet: 1.02 (0.21), residues: 516 loop : -0.79 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 107 HIS 0.003 0.001 HIS U 37 PHE 0.013 0.002 PHE A 225 TYR 0.015 0.001 TYR U 52 ARG 0.010 0.000 ARG B 596 *********************** 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 249 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 177 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7617 (mptp) REVERT: A 140 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7275 (mtpp) REVERT: B 514 ASN cc_start: 0.8232 (m110) cc_final: 0.7997 (m-40) REVERT: C 54 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6323 (tpm170) REVERT: C 144 THR cc_start: 0.8757 (p) cc_final: 0.8528 (p) REVERT: E 56 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7154 (tptt) REVERT: E 136 ARG cc_start: 0.7970 (mtp180) cc_final: 0.7749 (ttm-80) REVERT: E 140 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7243 (mtpm) REVERT: E 156 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7977 (mt-10) REVERT: O 7 GLN cc_start: 0.6703 (OUTLIER) cc_final: 0.6291 (mt0) REVERT: P 56 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7119 (m-30) outliers start: 72 outliers final: 41 residues processed: 227 average time/residue: 1.1936 time to fit residues: 294.5238 Evaluate side-chains 215 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain Y residue 60 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 90 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12360 Z= 0.233 Angle : 0.607 6.613 16800 Z= 0.316 Chirality : 0.047 0.445 1833 Planarity : 0.005 0.042 2187 Dihedral : 6.640 53.883 1854 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.46 % Allowed : 17.78 % Favored : 75.76 % 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: -0.01 (0.20), residues: 1536 helix: 1.40 (0.49), residues: 126 sheet: 1.00 (0.21), residues: 516 loop : -0.85 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS L 37 PHE 0.014 0.002 PHE A 225 TYR 0.014 0.001 TYR U 52 ARG 0.009 0.000 ARG B 596 *********************** 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 246 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 165 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7628 (mptp) REVERT: A 140 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7329 (mtpp) REVERT: B 514 ASN cc_start: 0.8276 (m110) cc_final: 0.8064 (m-40) REVERT: B 547 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8322 (tt) REVERT: D 547 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8268 (tt) REVERT: C 54 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.6225 (tpm170) REVERT: C 112 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: E 136 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7715 (ttm-80) REVERT: E 140 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7284 (mtpm) REVERT: E 156 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7991 (mt-10) REVERT: E 219 ARG cc_start: 0.7536 (mtp85) cc_final: 0.7088 (mtp180) REVERT: O 7 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.6291 (mt0) outliers start: 81 outliers final: 53 residues processed: 214 average time/residue: 1.1804 time to fit residues: 275.5930 Evaluate side-chains 220 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 159 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 60 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 90 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 chunk 132 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 E 61 ASN P 39 GLN ** 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: 0.7865 moved from start: 0.2881 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 : 0.549 6.284 16800 Z= 0.284 Chirality : 0.046 0.462 1833 Planarity : 0.004 0.039 2187 Dihedral : 6.000 52.419 1848 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.26 % Allowed : 19.22 % Favored : 75.52 % 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: -0.01 (0.20), residues: 1536 helix: 1.50 (0.49), residues: 126 sheet: 1.04 (0.21), residues: 480 loop : -0.83 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS C 154 PHE 0.013 0.001 PHE A 225 TYR 0.010 0.001 TYR U 52 ARG 0.013 0.000 ARG F 596 *********************** 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 234 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 168 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7615 (mptp) REVERT: A 136 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7655 (ttm170) REVERT: A 140 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7265 (mtpm) REVERT: B 514 ASN cc_start: 0.8267 (m110) cc_final: 0.8053 (m-40) REVERT: C 54 ARG cc_start: 0.6591 (OUTLIER) cc_final: 0.6175 (tpm170) REVERT: C 112 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: E 136 ARG cc_start: 0.7897 (mtp180) cc_final: 0.7668 (ttm170) REVERT: E 140 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7238 (mtpm) REVERT: E 156 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7942 (mt-10) REVERT: E 219 ARG cc_start: 0.7507 (mtp85) cc_final: 0.7071 (mtp180) REVERT: O 7 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.6260 (mt0) outliers start: 66 outliers final: 41 residues processed: 211 average time/residue: 1.0960 time to fit residues: 252.9716 Evaluate side-chains 209 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 162 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 90 THR Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 0.0020 chunk 142 optimal weight: 9.9990 overall best weight: 2.3194 ------------------------------------------------------------------------------- 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 C 228 ASN E 61 ASN P 39 GLN P 86 ASN Y 39 GLN Y 86 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12360 Z= 0.306 Angle : 0.643 7.054 16800 Z= 0.334 Chirality : 0.048 0.426 1833 Planarity : 0.005 0.045 2187 Dihedral : 6.181 56.217 1844 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.70 % Allowed : 18.82 % Favored : 74.48 % 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: 1.32 (0.49), residues: 126 sheet: 1.00 (0.21), residues: 507 loop : -0.98 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.004 0.001 HIS U 37 PHE 0.015 0.002 PHE A 225 TYR 0.016 0.002 TYR U 52 ARG 0.010 0.000 ARG B 596 *********************** 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 230 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 146 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7358 (mmm160) REVERT: H 43 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7550 (mptp) REVERT: A 140 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7368 (mtpm) REVERT: B 514 ASN cc_start: 0.8335 (m110) cc_final: 0.8119 (m-40) REVERT: D 547 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8299 (tt) REVERT: C 54 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.6179 (tpm170) REVERT: C 112 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: E 136 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7736 (ttm170) REVERT: E 140 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7350 (mtpp) REVERT: E 156 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7983 (mt-10) REVERT: O 7 GLN cc_start: 0.6670 (OUTLIER) cc_final: 0.6270 (mt0) REVERT: P 19 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7472 (mmm160) outliers start: 84 outliers final: 57 residues processed: 202 average time/residue: 1.1626 time to fit residues: 255.9885 Evaluate side-chains 208 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 142 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain P residue 19 ARG Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 90 THR Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 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 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: 0.7924 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12360 Z= 0.253 Angle : 0.602 7.208 16800 Z= 0.312 Chirality : 0.047 0.455 1833 Planarity : 0.005 0.049 2187 Dihedral : 6.018 55.678 1844 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 6.30 % Allowed : 19.06 % Favored : 74.64 % 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: 1.33 (0.49), residues: 126 sheet: 0.91 (0.21), residues: 510 loop : -1.01 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 47 HIS 0.003 0.001 HIS U 37 PHE 0.014 0.002 PHE A 225 TYR 0.014 0.001 TYR U 52 ARG 0.011 0.000 ARG F 596 *********************** 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 229 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 150 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7624 (mptp) REVERT: A 140 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7285 (mtpm) REVERT: B 547 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8305 (tt) REVERT: D 547 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8293 (tt) REVERT: C 54 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6172 (tpm170) REVERT: C 112 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: E 140 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7285 (mtpp) REVERT: E 156 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7972 (mt-10) REVERT: E 219 ARG cc_start: 0.7526 (mtp85) cc_final: 0.7095 (mtp180) REVERT: O 7 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6294 (mt0) REVERT: P 19 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7431 (mmm160) outliers start: 79 outliers final: 51 residues processed: 203 average time/residue: 1.1661 time to fit residues: 258.0226 Evaluate side-chains 208 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 148 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain P residue 19 ARG Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 90 THR Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 100 optimal weight: 0.3980 chunk 72 optimal weight: 30.0000 chunk 13 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 228 ASN C 61 ASN E 61 ASN P 39 GLN Y 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12360 Z= 0.182 Angle : 0.564 7.829 16800 Z= 0.291 Chirality : 0.046 0.456 1833 Planarity : 0.004 0.045 2187 Dihedral : 5.759 54.140 1842 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.42 % Allowed : 20.49 % Favored : 74.08 % 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: -0.15 (0.20), residues: 1536 helix: 1.50 (0.49), residues: 126 sheet: 1.01 (0.21), residues: 471 loop : -0.97 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS U 37 PHE 0.014 0.001 PHE A 225 TYR 0.011 0.001 TYR U 52 ARG 0.012 0.000 ARG F 596 *********************** 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 216 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 148 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7272 (mtpp) REVERT: C 54 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.6127 (tpm170) REVERT: E 140 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7205 (mtpm) REVERT: E 156 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7978 (mt-10) REVERT: E 219 ARG cc_start: 0.7510 (mtp85) cc_final: 0.7108 (mtp180) REVERT: O 7 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6248 (mt0) outliers start: 68 outliers final: 45 residues processed: 189 average time/residue: 1.1412 time to fit residues: 235.2394 Evaluate side-chains 194 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 145 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 90 THR Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 2.9990 chunk 137 optimal weight: 0.0060 chunk 141 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 129 optimal weight: 0.0980 chunk 136 optimal weight: 0.0770 chunk 90 optimal weight: 4.9990 overall best weight: 0.2954 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12360 Z= 0.126 Angle : 0.524 7.625 16800 Z= 0.266 Chirality : 0.046 0.469 1833 Planarity : 0.004 0.046 2187 Dihedral : 5.431 48.923 1841 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.47 % Allowed : 23.29 % Favored : 74.24 % 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: 1.66 (0.48), residues: 126 sheet: 0.58 (0.21), residues: 537 loop : -0.75 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 33 HIS 0.001 0.000 HIS C 154 PHE 0.011 0.001 PHE E 225 TYR 0.007 0.001 TYR U 52 ARG 0.011 0.000 ARG F 596 *********************** 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 198 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 596 ARG cc_start: 0.7565 (mtt90) cc_final: 0.7236 (mmt90) REVERT: C 54 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.6161 (tpm170) REVERT: E 140 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7209 (mtpm) REVERT: E 156 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7949 (mt-10) outliers start: 31 outliers final: 21 residues processed: 183 average time/residue: 1.1504 time to fit residues: 230.1446 Evaluate side-chains 174 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 90 THR Chi-restraints excluded: chain Y residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 121 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- 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: 0.7871 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12360 Z= 0.183 Angle : 0.553 7.079 16800 Z= 0.282 Chirality : 0.045 0.429 1833 Planarity : 0.004 0.045 2187 Dihedral : 5.479 49.979 1841 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.31 % Allowed : 23.52 % Favored : 74.16 % 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: -0.07 (0.20), residues: 1536 helix: 1.67 (0.48), residues: 126 sheet: 0.65 (0.20), residues: 564 loop : -0.81 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 47 HIS 0.002 0.001 HIS L 37 PHE 0.013 0.001 PHE A 225 TYR 0.009 0.001 TYR U 52 ARG 0.011 0.000 ARG F 596 ********************** 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 170 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.6237 (tpm170) REVERT: E 140 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7235 (mtpm) REVERT: E 156 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7948 (mt-10) outliers start: 29 outliers final: 24 residues processed: 159 average time/residue: 1.2576 time to fit residues: 217.2729 Evaluate side-chains 167 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 90 THR Chi-restraints excluded: chain Y residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 111 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 121 optimal weight: 0.0770 chunk 50 optimal weight: 40.0000 chunk 124 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 0.4980 overall best weight: 0.9740 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.181765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.144454 restraints weight = 13735.957| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.74 r_work: 0.3298 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3383 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= 0.166 Angle : 0.545 7.047 16800 Z= 0.277 Chirality : 0.045 0.441 1833 Planarity : 0.004 0.046 2187 Dihedral : 5.413 49.284 1841 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.55 % Allowed : 23.21 % Favored : 74.24 % 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: -0.02 (0.20), residues: 1536 helix: 1.72 (0.48), residues: 126 sheet: 0.67 (0.21), residues: 537 loop : -0.71 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS U 37 PHE 0.013 0.001 PHE A 225 TYR 0.007 0.001 TYR U 52 ARG 0.011 0.000 ARG F 596 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4549.00 seconds wall clock time: 81 minutes 33.05 seconds (4893.05 seconds total)