Starting phenix.real_space_refine on Sat Mar 16 06:07:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/03_2024/7kej_22839.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/03_2024/7kej_22839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/03_2024/7kej_22839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/03_2024/7kej_22839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/03_2024/7kej_22839.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/03_2024/7kej_22839.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 8718 2.51 5 N 2322 2.21 5 O 2709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 545": "OE1" <-> "OE2" Residue "E PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 545": "OE1" <-> "OE2" Residue "F PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "D PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13806 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 984 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "K" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "C" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 984 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "A" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "G" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 984 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "J" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.52, per 1000 atoms: 0.54 Number of scatterers: 13806 At special positions: 0 Unit cell: (156.56, 160.68, 124.63, 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 57 16.00 O 2709 8.00 N 2322 7.00 C 8718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.04 Simple disulfide: pdb=" SG CYS E 601 " - pdb=" SG CYS E 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 87 " distance=2.03 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=2.03 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 ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 401 " - " ASN A 257 " " NAG A 402 " - " ASN A 268 " " NAG A 403 " - " ASN A 228 " " NAG B 401 " - " ASN B 257 " " NAG B 402 " - " ASN B 268 " " NAG B 403 " - " ASN B 228 " " NAG C 401 " - " ASN C 257 " " NAG C 402 " - " ASN C 268 " " NAG C 403 " - " ASN C 228 " " NAG M 1 " - " ASN E 563 " " NAG N 1 " - " ASN F 563 " " NAG O 1 " - " ASN D 563 " Time building additional restraints: 5.44 Conformation dependent library (CDL) restraints added in 2.3 seconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 30 sheets defined 15.7% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 25 through 28 Processing helix chain 'K' and resid 78 through 82 Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 553 through 575 removed outlier: 4.848A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 598 removed outlier: 3.845A pdb=" N ARG E 596 " --> pdb=" O PHE E 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 83 Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'L' and resid 25 through 28 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 553 through 575 removed outlier: 4.847A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.845A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (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 83 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'J' and resid 25 through 28 Processing helix chain 'J' and resid 78 through 82 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 553 through 575 removed outlier: 4.847A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.845A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 36 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 36 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 114 removed outlier: 6.405A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG B 136 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 14.122A pdb=" N THR B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ASP B 237 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 277 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN B 243 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE B 274 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASN H 101 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.070A pdb=" N CYS H 96 " --> pdb=" O TRP H 118 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TRP H 118 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG H 98 " --> pdb=" O ASP H 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU K 108 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL K 12 " --> pdb=" O LEU K 108 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP K 34 " --> pdb=" O VAL K 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU K 108 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL K 12 " --> pdb=" O LEU K 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AB1, first strand: chain 'E' and resid 601 through 602 removed outlier: 6.641A pdb=" N CYS E 601 " --> pdb=" O GLU F 611 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 610 through 611 Processing sheet with id=AB3, first strand: chain 'C' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB6, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.405A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 14.122A pdb=" N THR C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ASP C 237 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL C 277 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN C 243 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE C 274 " --> pdb=" O GLN I 99 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASN I 101 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.070A pdb=" N CYS I 96 " --> pdb=" O TRP I 118 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP I 118 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG I 98 " --> pdb=" O ASP I 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU L 108 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL L 12 " --> pdb=" O LEU L 108 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU L 108 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL L 12 " --> pdb=" O LEU L 108 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AC3, first strand: chain 'F' and resid 601 through 602 removed outlier: 6.641A pdb=" N CYS F 601 " --> pdb=" O GLU D 611 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AC7, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.405A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 14.122A pdb=" N THR A 217 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ASP A 237 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A 277 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN A 243 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE A 274 " --> pdb=" O GLN G 99 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN G 101 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 7.070A pdb=" N CYS G 96 " --> pdb=" O TRP G 118 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP G 118 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG G 98 " --> pdb=" O ASP G 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'J' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU J 108 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL J 12 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP J 34 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU J 108 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL J 12 " --> pdb=" O LEU J 108 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 18 through 23 532 hydrogen bonds defined for protein. 1290 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: 4.13 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2797 1.32 - 1.45: 4352 1.45 - 1.58: 6842 1.58 - 1.72: 55 1.72 - 1.85: 69 Bond restraints: 14115 Sorted by residual: bond pdb=" CB HIS C 154 " pdb=" CG HIS C 154 " ideal model delta sigma weight residual 1.497 1.404 0.093 1.40e-02 5.10e+03 4.41e+01 bond pdb=" CB HIS B 154 " pdb=" CG HIS B 154 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.35e+01 bond pdb=" CB HIS A 154 " pdb=" CG HIS A 154 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.33e+01 bond pdb=" CB TYR B 99 " pdb=" CG TYR B 99 " ideal model delta sigma weight residual 1.512 1.381 0.131 2.20e-02 2.07e+03 3.53e+01 bond pdb=" CB TYR C 99 " pdb=" CG TYR C 99 " ideal model delta sigma weight residual 1.512 1.381 0.131 2.20e-02 2.07e+03 3.52e+01 ... (remaining 14110 not shown) Histogram of bond angle deviations from ideal: 101.26 - 107.81: 953 107.81 - 114.36: 7267 114.36 - 120.91: 6490 120.91 - 127.46: 4325 127.46 - 134.01: 144 Bond angle restraints: 19179 Sorted by residual: angle pdb=" N ARG K 60 " pdb=" CA ARG K 60 " pdb=" C ARG K 60 " ideal model delta sigma weight residual 114.56 103.35 11.21 1.27e+00 6.20e-01 7.79e+01 angle pdb=" N ARG J 60 " pdb=" CA ARG J 60 " pdb=" C ARG J 60 " ideal model delta sigma weight residual 114.56 103.37 11.19 1.27e+00 6.20e-01 7.76e+01 angle pdb=" N ARG L 60 " pdb=" CA ARG L 60 " pdb=" C ARG L 60 " ideal model delta sigma weight residual 114.56 103.37 11.19 1.27e+00 6.20e-01 7.76e+01 angle pdb=" C LEU B 122 " pdb=" N PRO B 123 " pdb=" CA PRO B 123 " ideal model delta sigma weight residual 119.85 127.15 -7.30 1.01e+00 9.80e-01 5.23e+01 angle pdb=" C LEU C 122 " pdb=" N PRO C 123 " pdb=" CA PRO C 123 " ideal model delta sigma weight residual 119.85 127.14 -7.29 1.01e+00 9.80e-01 5.21e+01 ... (remaining 19174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 8340 21.17 - 42.35: 171 42.35 - 63.52: 39 63.52 - 84.70: 30 84.70 - 105.87: 21 Dihedral angle restraints: 8601 sinusoidal: 3645 harmonic: 4956 Sorted by residual: dihedral pdb=" CB CYS B 108 " pdb=" SG CYS B 108 " pdb=" SG CYS B 135 " pdb=" CB CYS B 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.12 -37.12 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS C 108 " pdb=" SG CYS C 108 " pdb=" SG CYS C 135 " pdb=" CB CYS C 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.11 -37.11 1 1.00e+01 1.00e-02 1.94e+01 dihedral pdb=" CB CYS A 108 " pdb=" SG CYS A 108 " pdb=" SG CYS A 135 " pdb=" CB CYS A 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.11 -37.11 1 1.00e+01 1.00e-02 1.94e+01 ... (remaining 8598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1529 0.094 - 0.187: 507 0.187 - 0.281: 92 0.281 - 0.375: 34 0.375 - 0.468: 25 Chirality restraints: 2187 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.02e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 ... (remaining 2184 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 228 " -0.045 2.00e-02 2.50e+03 4.88e-02 2.98e+01 pdb=" CG ASN C 228 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN C 228 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 228 " 0.079 2.00e-02 2.50e+03 pdb=" C1 NAG C 403 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 228 " 0.045 2.00e-02 2.50e+03 4.86e-02 2.96e+01 pdb=" CG ASN B 228 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 228 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 228 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG B 403 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 228 " 0.045 2.00e-02 2.50e+03 4.86e-02 2.95e+01 pdb=" CG ASN A 228 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 228 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 228 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG A 403 " 0.058 2.00e-02 2.50e+03 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 3 1.94 - 2.68: 491 2.68 - 3.42: 17447 3.42 - 4.16: 34283 4.16 - 4.90: 57572 Nonbonded interactions: 109796 Sorted by model distance: nonbonded pdb=" OE1 GLU G 102 " pdb=" OH TYR G 112 " model vdw 1.201 2.440 nonbonded pdb=" OE1 GLU H 102 " pdb=" OH TYR H 112 " model vdw 1.201 2.440 nonbonded pdb=" OE1 GLU I 102 " pdb=" OH TYR I 112 " model vdw 1.202 2.440 nonbonded pdb=" CD GLU G 102 " pdb=" OH TYR G 112 " model vdw 2.293 3.270 nonbonded pdb=" CD GLU I 102 " pdb=" OH TYR I 112 " model vdw 2.293 3.270 ... (remaining 109791 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.600 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 37.140 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.021 0.148 14115 Z= 1.348 Angle : 1.725 11.208 19179 Z= 1.152 Chirality : 0.107 0.468 2187 Planarity : 0.008 0.038 2442 Dihedral : 11.824 105.871 5391 Min Nonbonded Distance : 1.201 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.19), residues: 1704 helix: 1.45 (0.35), residues: 156 sheet: 0.90 (0.20), residues: 594 loop : 0.77 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.008 TRP A 86 HIS 0.006 0.002 HIS D 602 PHE 0.020 0.005 PHE C 248 TYR 0.066 0.009 TYR B 99 ARG 0.006 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 ARG cc_start: 0.7902 (tpt90) cc_final: 0.7629 (mpt-90) REVERT: H 13 LYS cc_start: 0.7170 (mttm) cc_final: 0.6827 (mppt) REVERT: H 115 MET cc_start: 0.8962 (mpp) cc_final: 0.8641 (mpp) REVERT: K 16 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6179 (tm-30) REVERT: K 17 THR cc_start: 0.8371 (m) cc_final: 0.7928 (m) REVERT: K 30 TYR cc_start: 0.6837 (m-80) cc_final: 0.6620 (m-80) REVERT: K 74 ILE cc_start: 0.8975 (mt) cc_final: 0.8748 (mt) REVERT: K 91 ASP cc_start: 0.8784 (t0) cc_final: 0.8580 (t0) REVERT: E 527 ILE cc_start: 0.7701 (mm) cc_final: 0.7351 (pt) REVERT: C 278 ASN cc_start: 0.8247 (t0) cc_final: 0.8039 (t0) REVERT: C 281 ILE cc_start: 0.7935 (pt) cc_final: 0.7572 (pt) REVERT: I 13 LYS cc_start: 0.7176 (mttm) cc_final: 0.6767 (mptt) REVERT: I 115 MET cc_start: 0.9000 (mpp) cc_final: 0.8683 (mpp) REVERT: L 16 GLN cc_start: 0.7097 (mm-40) cc_final: 0.6605 (tt0) REVERT: L 28 ARG cc_start: 0.7445 (mtt-85) cc_final: 0.7243 (ttm110) REVERT: L 51 ASN cc_start: 0.8398 (p0) cc_final: 0.8163 (p0) REVERT: L 91 ASP cc_start: 0.8757 (t0) cc_final: 0.8519 (t0) REVERT: F 527 ILE cc_start: 0.7826 (mm) cc_final: 0.7593 (pt) REVERT: F 588 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8900 (mmtp) REVERT: G 13 LYS cc_start: 0.7393 (mttm) cc_final: 0.6930 (mppt) REVERT: G 115 MET cc_start: 0.8951 (mpp) cc_final: 0.8661 (mpp) REVERT: J 16 GLN cc_start: 0.7201 (mm-40) cc_final: 0.6218 (tm-30) REVERT: J 91 ASP cc_start: 0.8823 (t0) cc_final: 0.8595 (t0) REVERT: D 527 ILE cc_start: 0.7508 (mm) cc_final: 0.7250 (pt) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.2834 time to fit residues: 146.3683 Evaluate side-chains 187 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14115 Z= 0.212 Angle : 0.625 9.394 19179 Z= 0.337 Chirality : 0.047 0.295 2187 Planarity : 0.004 0.070 2442 Dihedral : 9.067 80.654 2370 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.93 % Allowed : 7.94 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.19), residues: 1704 helix: 2.31 (0.38), residues: 159 sheet: 0.55 (0.19), residues: 645 loop : 0.56 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 86 HIS 0.006 0.001 HIS L 96 PHE 0.017 0.002 PHE F 592 TYR 0.022 0.002 TYR B 261 ARG 0.006 0.001 ARG J 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 228 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.7389 (mttm) cc_final: 0.6983 (mptt) REVERT: H 81 MET cc_start: 0.7554 (tmm) cc_final: 0.6768 (tmm) REVERT: H 82 GLU cc_start: 0.8450 (tp30) cc_final: 0.7885 (tp30) REVERT: K 16 GLN cc_start: 0.7168 (mm-40) cc_final: 0.6252 (tm-30) REVERT: K 57 ILE cc_start: 0.8314 (mm) cc_final: 0.8060 (tp) REVERT: K 97 LEU cc_start: 0.9184 (tp) cc_final: 0.8893 (tp) REVERT: E 527 ILE cc_start: 0.7968 (mm) cc_final: 0.7547 (pt) REVERT: E 611 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6563 (mm-30) REVERT: C 281 ILE cc_start: 0.7892 (pt) cc_final: 0.7657 (pt) REVERT: I 13 LYS cc_start: 0.7310 (mttm) cc_final: 0.6909 (mptt) REVERT: I 48 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6349 (ttm) REVERT: L 16 GLN cc_start: 0.7050 (mm-40) cc_final: 0.6679 (tt0) REVERT: L 35 TYR cc_start: 0.9080 (m-80) cc_final: 0.8839 (m-80) REVERT: L 51 ASN cc_start: 0.8235 (p0) cc_final: 0.7968 (p0) REVERT: F 527 ILE cc_start: 0.7952 (mm) cc_final: 0.7683 (pt) REVERT: G 13 LYS cc_start: 0.7310 (mttm) cc_final: 0.6907 (mppt) REVERT: G 81 MET cc_start: 0.8312 (tmm) cc_final: 0.7891 (tmm) REVERT: J 6 GLN cc_start: 0.6695 (mt0) cc_final: 0.6373 (mt0) REVERT: J 16 GLN cc_start: 0.7154 (mm-40) cc_final: 0.6291 (tm-30) REVERT: J 17 THR cc_start: 0.8424 (m) cc_final: 0.7974 (m) REVERT: D 527 ILE cc_start: 0.7860 (mm) cc_final: 0.7590 (pt) REVERT: D 602 HIS cc_start: 0.6003 (OUTLIER) cc_final: 0.4881 (t-90) outliers start: 28 outliers final: 18 residues processed: 241 average time/residue: 0.2316 time to fit residues: 83.7324 Evaluate side-chains 205 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 68 ASN Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN E 551 GLN E 595 GLN C 44 GLN I 65 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN D 551 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14115 Z= 0.269 Angle : 0.591 8.076 19179 Z= 0.315 Chirality : 0.045 0.222 2187 Planarity : 0.004 0.042 2442 Dihedral : 8.190 71.800 2370 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.35 % Allowed : 9.18 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.19), residues: 1704 helix: 1.80 (0.40), residues: 177 sheet: 0.45 (0.19), residues: 621 loop : 0.21 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 86 HIS 0.018 0.002 HIS D 602 PHE 0.016 0.002 PHE B 159 TYR 0.012 0.001 TYR L 30 ARG 0.005 0.001 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: H 13 LYS cc_start: 0.7459 (mttm) cc_final: 0.6923 (mptt) REVERT: H 81 MET cc_start: 0.7683 (tmm) cc_final: 0.6777 (tmm) REVERT: K 16 GLN cc_start: 0.7275 (mm-40) cc_final: 0.6271 (tm-30) REVERT: E 527 ILE cc_start: 0.8203 (mm) cc_final: 0.7849 (pt) REVERT: C 281 ILE cc_start: 0.7911 (pt) cc_final: 0.7680 (pt) REVERT: I 13 LYS cc_start: 0.7531 (mttm) cc_final: 0.6977 (mptt) REVERT: I 48 MET cc_start: 0.7325 (mtm) cc_final: 0.6649 (ttm) REVERT: I 115 MET cc_start: 0.8819 (mpp) cc_final: 0.7969 (mpp) REVERT: L 16 GLN cc_start: 0.7297 (mm-40) cc_final: 0.6767 (tt0) REVERT: F 552 ASP cc_start: 0.7792 (t0) cc_final: 0.7429 (t0) REVERT: A 100 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: G 13 LYS cc_start: 0.7562 (mttm) cc_final: 0.6906 (mppt) REVERT: G 81 MET cc_start: 0.8393 (tmm) cc_final: 0.7480 (tmm) REVERT: J 6 GLN cc_start: 0.6628 (mt0) cc_final: 0.6401 (mt0) REVERT: J 16 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6346 (tm-30) REVERT: J 17 THR cc_start: 0.8408 (m) cc_final: 0.8003 (m) REVERT: D 527 ILE cc_start: 0.8037 (mm) cc_final: 0.7817 (pt) REVERT: D 552 ASP cc_start: 0.7684 (t0) cc_final: 0.7475 (t0) outliers start: 34 outliers final: 23 residues processed: 214 average time/residue: 0.2323 time to fit residues: 75.2195 Evaluate side-chains 198 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 25 ASP Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 84 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 0.0020 chunk 153 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 GLN A 243 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 GLN ** D 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14115 Z= 0.407 Angle : 0.665 10.648 19179 Z= 0.346 Chirality : 0.049 0.241 2187 Planarity : 0.005 0.052 2442 Dihedral : 7.565 57.950 2370 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.59 % Allowed : 9.32 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.19), residues: 1704 helix: 1.56 (0.39), residues: 177 sheet: 0.20 (0.20), residues: 630 loop : -0.12 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.005 0.001 HIS K 96 PHE 0.023 0.003 PHE C 159 TYR 0.014 0.002 TYR A 220 ARG 0.006 0.001 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 202 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: B 48 VAL cc_start: 0.8071 (t) cc_final: 0.7661 (p) REVERT: B 50 LYS cc_start: 0.8293 (tttt) cc_final: 0.7903 (pttt) REVERT: B 100 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: B 161 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9053 (mt) REVERT: H 13 LYS cc_start: 0.7362 (mttm) cc_final: 0.6810 (mppt) REVERT: H 81 MET cc_start: 0.7863 (tmm) cc_final: 0.7014 (tmm) REVERT: K 4 LEU cc_start: 0.7842 (mp) cc_final: 0.7576 (mt) REVERT: K 16 GLN cc_start: 0.7378 (mm-40) cc_final: 0.6940 (tt0) REVERT: C 100 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: C 161 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8991 (mt) REVERT: C 281 ILE cc_start: 0.7975 (pt) cc_final: 0.7762 (pt) REVERT: I 13 LYS cc_start: 0.7472 (mttm) cc_final: 0.6846 (mptt) REVERT: L 16 GLN cc_start: 0.7391 (mm-40) cc_final: 0.7000 (tt0) REVERT: L 35 TYR cc_start: 0.9006 (m-80) cc_final: 0.8764 (m-80) REVERT: L 40 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.8039 (mtm-85) REVERT: F 551 GLN cc_start: 0.8051 (mm110) cc_final: 0.7727 (mm-40) REVERT: F 552 ASP cc_start: 0.8035 (t0) cc_final: 0.7711 (t0) REVERT: A 100 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: A 161 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9207 (mt) REVERT: G 13 LYS cc_start: 0.7593 (mttm) cc_final: 0.6899 (mppt) REVERT: G 81 MET cc_start: 0.8427 (tmm) cc_final: 0.7516 (tmm) REVERT: J 16 GLN cc_start: 0.7336 (mm-40) cc_final: 0.6955 (tt0) outliers start: 52 outliers final: 34 residues processed: 235 average time/residue: 0.2359 time to fit residues: 82.9112 Evaluate side-chains 218 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 178 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 545 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 545 GLU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14115 Z= 0.349 Angle : 0.604 8.099 19179 Z= 0.316 Chirality : 0.046 0.234 2187 Planarity : 0.005 0.039 2442 Dihedral : 7.085 49.640 2370 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.04 % Allowed : 11.04 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.19), residues: 1704 helix: 1.59 (0.39), residues: 177 sheet: 0.09 (0.20), residues: 627 loop : -0.24 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.004 0.001 HIS K 96 PHE 0.016 0.002 PHE A 159 TYR 0.012 0.002 TYR A 109 ARG 0.007 0.001 ARG K 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 VAL cc_start: 0.8039 (t) cc_final: 0.7691 (p) REVERT: B 50 LYS cc_start: 0.8324 (tttt) cc_final: 0.7900 (pttt) REVERT: B 100 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: B 161 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9114 (mt) REVERT: H 13 LYS cc_start: 0.7301 (mttm) cc_final: 0.6740 (mptt) REVERT: H 81 MET cc_start: 0.7818 (tmm) cc_final: 0.6901 (tmm) REVERT: K 4 LEU cc_start: 0.7956 (mp) cc_final: 0.7338 (mt) REVERT: K 16 GLN cc_start: 0.7450 (mm-40) cc_final: 0.7095 (tt0) REVERT: E 551 GLN cc_start: 0.7809 (mm110) cc_final: 0.7556 (mm110) REVERT: I 13 LYS cc_start: 0.7452 (mttm) cc_final: 0.6777 (mptt) REVERT: I 48 MET cc_start: 0.7525 (mtm) cc_final: 0.6982 (ttm) REVERT: I 82 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8437 (mm-30) REVERT: I 115 MET cc_start: 0.8731 (mpp) cc_final: 0.8171 (mpp) REVERT: L 16 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7234 (tt0) REVERT: F 552 ASP cc_start: 0.8052 (t0) cc_final: 0.7727 (t0) REVERT: A 100 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: G 10 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8060 (mm-30) REVERT: G 13 LYS cc_start: 0.7598 (mttm) cc_final: 0.6897 (mppt) REVERT: J 16 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7151 (tt0) outliers start: 44 outliers final: 28 residues processed: 230 average time/residue: 0.2252 time to fit residues: 78.5575 Evaluate side-chains 215 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 514 ASN Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 601 CYS Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 68 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 601 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 40 optimal weight: 0.0010 chunk 162 optimal weight: 0.9990 chunk 134 optimal weight: 0.0980 chunk 75 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS F 551 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14115 Z= 0.143 Angle : 0.526 9.396 19179 Z= 0.272 Chirality : 0.044 0.232 2187 Planarity : 0.004 0.030 2442 Dihedral : 6.398 59.588 2370 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.35 % Allowed : 12.63 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.20), residues: 1704 helix: 1.91 (0.40), residues: 177 sheet: 0.14 (0.20), residues: 633 loop : -0.11 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 34 HIS 0.003 0.001 HIS L 96 PHE 0.008 0.001 PHE G 29 TYR 0.010 0.001 TYR B 109 ARG 0.005 0.000 ARG J 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.8263 (tttt) cc_final: 0.7879 (pttt) REVERT: B 100 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: H 13 LYS cc_start: 0.7332 (mttm) cc_final: 0.6774 (mptt) REVERT: K 16 GLN cc_start: 0.7469 (mm-40) cc_final: 0.7168 (tt0) REVERT: K 40 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.7986 (mtt90) REVERT: C 100 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: I 10 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8046 (mm-30) REVERT: I 13 LYS cc_start: 0.7484 (mttm) cc_final: 0.6822 (mptt) REVERT: I 48 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.7061 (ttm) REVERT: I 115 MET cc_start: 0.8675 (mpp) cc_final: 0.8093 (mpp) REVERT: L 16 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7327 (tt0) REVERT: L 88 ASN cc_start: 0.9289 (t0) cc_final: 0.8860 (t0) REVERT: F 552 ASP cc_start: 0.7997 (t0) cc_final: 0.7663 (t0) REVERT: A 100 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6648 (mp0) REVERT: G 10 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8060 (mm-30) REVERT: G 13 LYS cc_start: 0.7566 (mttm) cc_final: 0.6736 (mmtp) REVERT: G 82 GLU cc_start: 0.8785 (tp30) cc_final: 0.8502 (tp30) outliers start: 34 outliers final: 25 residues processed: 214 average time/residue: 0.2434 time to fit residues: 77.6975 Evaluate side-chains 214 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 92 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 14115 Z= 0.410 Angle : 0.632 8.768 19179 Z= 0.330 Chirality : 0.047 0.201 2187 Planarity : 0.005 0.040 2442 Dihedral : 6.084 48.864 2370 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.04 % Allowed : 13.04 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1704 helix: 1.77 (0.39), residues: 177 sheet: -0.00 (0.20), residues: 633 loop : -0.30 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.005 0.001 HIS K 96 PHE 0.020 0.002 PHE H 29 TYR 0.013 0.002 TYR K 35 ARG 0.009 0.001 ARG L 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 195 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 VAL cc_start: 0.8069 (t) cc_final: 0.7718 (p) REVERT: B 50 LYS cc_start: 0.8418 (tttt) cc_final: 0.7901 (pttt) REVERT: B 100 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: B 161 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9122 (mt) REVERT: H 13 LYS cc_start: 0.7355 (mttm) cc_final: 0.6775 (mptt) REVERT: H 81 MET cc_start: 0.7644 (tmm) cc_final: 0.6993 (tmm) REVERT: K 16 GLN cc_start: 0.7515 (mm-40) cc_final: 0.7221 (tt0) REVERT: E 551 GLN cc_start: 0.7724 (mm110) cc_final: 0.7435 (mm110) REVERT: C 100 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: I 10 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7997 (mm-30) REVERT: I 13 LYS cc_start: 0.7373 (mttm) cc_final: 0.6646 (mptt) REVERT: I 82 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8387 (mm-30) REVERT: L 16 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7274 (tt0) REVERT: F 552 ASP cc_start: 0.8147 (t0) cc_final: 0.7817 (t0) REVERT: A 100 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: G 10 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8127 (mm-30) REVERT: G 13 LYS cc_start: 0.7551 (mttm) cc_final: 0.6830 (mppt) REVERT: G 82 GLU cc_start: 0.8831 (tp30) cc_final: 0.8542 (tp30) outliers start: 44 outliers final: 32 residues processed: 222 average time/residue: 0.2389 time to fit residues: 79.6850 Evaluate side-chains 219 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 514 ASN Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 601 CYS Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 0.1980 chunk 127 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14115 Z= 0.172 Angle : 0.530 9.500 19179 Z= 0.278 Chirality : 0.043 0.194 2187 Planarity : 0.004 0.032 2442 Dihedral : 5.330 43.831 2370 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.35 % Allowed : 14.08 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1704 helix: 1.52 (0.38), residues: 195 sheet: 0.20 (0.20), residues: 645 loop : -0.35 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 34 HIS 0.003 0.001 HIS H 110 PHE 0.010 0.001 PHE H 29 TYR 0.010 0.001 TYR A 99 ARG 0.007 0.000 ARG F 596 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 VAL cc_start: 0.8064 (t) cc_final: 0.7716 (p) REVERT: B 50 LYS cc_start: 0.8389 (tttt) cc_final: 0.7937 (pttt) REVERT: B 100 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: H 13 LYS cc_start: 0.7359 (mttm) cc_final: 0.6777 (mptt) REVERT: H 81 MET cc_start: 0.7467 (tmm) cc_final: 0.6830 (tmm) REVERT: H 82 GLU cc_start: 0.8817 (tp30) cc_final: 0.8244 (tp30) REVERT: H 89 GLU cc_start: 0.7917 (pm20) cc_final: 0.7619 (pm20) REVERT: E 551 GLN cc_start: 0.7669 (mm110) cc_final: 0.7431 (mm110) REVERT: C 100 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: I 10 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7997 (mm-30) REVERT: I 13 LYS cc_start: 0.7365 (mttm) cc_final: 0.6680 (mptt) REVERT: I 82 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8317 (mm-30) REVERT: L 104 LYS cc_start: 0.8562 (tppt) cc_final: 0.8334 (tppt) REVERT: F 552 ASP cc_start: 0.8086 (t0) cc_final: 0.7776 (t0) REVERT: A 100 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: G 10 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8112 (mm-30) REVERT: G 13 LYS cc_start: 0.7614 (mttm) cc_final: 0.6732 (mmtp) REVERT: G 60 TYR cc_start: 0.7742 (m-80) cc_final: 0.7413 (m-80) REVERT: G 82 GLU cc_start: 0.8767 (tp30) cc_final: 0.8425 (mm-30) outliers start: 34 outliers final: 24 residues processed: 216 average time/residue: 0.2522 time to fit residues: 81.9704 Evaluate side-chains 208 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 601 CYS Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 GLN K 41 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN G 65 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 14115 Z= 0.514 Angle : 0.677 8.928 19179 Z= 0.356 Chirality : 0.048 0.205 2187 Planarity : 0.006 0.047 2442 Dihedral : 6.111 46.871 2370 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.35 % Allowed : 14.35 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.20), residues: 1704 helix: 1.27 (0.37), residues: 195 sheet: -0.07 (0.20), residues: 660 loop : -0.58 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 104 HIS 0.005 0.001 HIS K 96 PHE 0.021 0.003 PHE A 159 TYR 0.013 0.002 TYR A 220 ARG 0.007 0.001 ARG E 580 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 189 time to evaluate : 2.457 Fit side-chains revert: symmetry clash REVERT: B 50 LYS cc_start: 0.8388 (tttt) cc_final: 0.7923 (pttt) REVERT: B 100 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: B 161 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9140 (mt) REVERT: H 13 LYS cc_start: 0.7256 (mttm) cc_final: 0.6677 (mppt) REVERT: H 81 MET cc_start: 0.7747 (tmm) cc_final: 0.6909 (tmm) REVERT: H 89 GLU cc_start: 0.7975 (pm20) cc_final: 0.7737 (pm20) REVERT: E 551 GLN cc_start: 0.7898 (mm110) cc_final: 0.7593 (mm110) REVERT: C 100 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: I 13 LYS cc_start: 0.7304 (mttm) cc_final: 0.6547 (mptt) REVERT: I 82 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8339 (mm-30) REVERT: L 104 LYS cc_start: 0.8701 (tppt) cc_final: 0.8419 (tppt) REVERT: F 552 ASP cc_start: 0.8138 (t0) cc_final: 0.7825 (t0) REVERT: A 100 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: G 13 LYS cc_start: 0.7596 (mttm) cc_final: 0.6840 (mppt) REVERT: G 60 TYR cc_start: 0.7770 (m-80) cc_final: 0.7416 (m-80) REVERT: G 82 GLU cc_start: 0.8826 (tp30) cc_final: 0.8501 (tp30) REVERT: D 551 GLN cc_start: 0.7620 (mm110) cc_final: 0.7388 (mm-40) outliers start: 34 outliers final: 26 residues processed: 210 average time/residue: 0.2477 time to fit residues: 79.2872 Evaluate side-chains 216 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 105 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14115 Z= 0.188 Angle : 0.549 10.059 19179 Z= 0.289 Chirality : 0.044 0.198 2187 Planarity : 0.004 0.033 2442 Dihedral : 5.549 46.734 2370 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.93 % Allowed : 14.70 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1704 helix: 1.49 (0.38), residues: 195 sheet: 0.02 (0.20), residues: 660 loop : -0.50 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 34 HIS 0.002 0.001 HIS L 96 PHE 0.009 0.001 PHE H 29 TYR 0.014 0.001 TYR K 35 ARG 0.006 0.001 ARG F 596 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.8358 (tttt) cc_final: 0.7906 (pttt) REVERT: B 100 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: B 161 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9101 (mt) REVERT: H 10 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8033 (mm-30) REVERT: H 13 LYS cc_start: 0.7362 (mttm) cc_final: 0.6777 (mppt) REVERT: H 81 MET cc_start: 0.7504 (tmm) cc_final: 0.6876 (tmm) REVERT: H 82 GLU cc_start: 0.8826 (tp30) cc_final: 0.8350 (tp30) REVERT: E 551 GLN cc_start: 0.7877 (mm110) cc_final: 0.7539 (mm-40) REVERT: C 100 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: I 10 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8030 (mm-30) REVERT: I 13 LYS cc_start: 0.7326 (mttm) cc_final: 0.6614 (mptt) REVERT: I 82 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8336 (mm-30) REVERT: L 104 LYS cc_start: 0.8658 (tppt) cc_final: 0.8416 (tppt) REVERT: F 552 ASP cc_start: 0.7941 (t0) cc_final: 0.7696 (t0) REVERT: A 100 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: A 288 TRP cc_start: 0.7242 (m100) cc_final: 0.6712 (m-10) REVERT: G 10 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8334 (mm-30) REVERT: G 13 LYS cc_start: 0.7565 (mttm) cc_final: 0.6674 (mmtp) REVERT: G 60 TYR cc_start: 0.7718 (m-80) cc_final: 0.7366 (m-80) REVERT: G 82 GLU cc_start: 0.8812 (tp30) cc_final: 0.8458 (tp30) REVERT: G 89 GLU cc_start: 0.8003 (pm20) cc_final: 0.7648 (pm20) REVERT: D 551 GLN cc_start: 0.7639 (mm110) cc_final: 0.7425 (mm-40) outliers start: 28 outliers final: 24 residues processed: 209 average time/residue: 0.2276 time to fit residues: 72.1015 Evaluate side-chains 209 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 181 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain F residue 514 ASN Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.097668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.076889 restraints weight = 29443.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.078307 restraints weight = 57451.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.078701 restraints weight = 41582.332| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14115 Z= 0.308 Angle : 0.583 9.784 19179 Z= 0.306 Chirality : 0.045 0.197 2187 Planarity : 0.004 0.037 2442 Dihedral : 5.641 47.099 2370 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.28 % Allowed : 14.63 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1704 helix: 1.51 (0.38), residues: 195 sheet: 0.10 (0.20), residues: 645 loop : -0.59 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 34 HIS 0.003 0.001 HIS K 96 PHE 0.021 0.002 PHE G 29 TYR 0.015 0.002 TYR I 60 ARG 0.005 0.001 ARG F 596 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2493.23 seconds wall clock time: 48 minutes 27.37 seconds (2907.37 seconds total)