Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 01:44:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/04_2023/7kej_22839.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/04_2023/7kej_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_22839/04_2023/7kej_22839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/04_2023/7kej_22839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/04_2023/7kej_22839.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kej_22839/04_2023/7kej_22839.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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-1.21rc1-4938/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 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 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 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 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 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 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: 5.85 Conformation dependent library (CDL) restraints added in 2.1 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: 1.02 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: 4.45 Time building geometry restraints manager: 6.25 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 - 17.76: 7863 17.76 - 35.53: 174 35.53 - 53.29: 42 53.29 - 71.05: 21 71.05 - 88.82: 15 Dihedral angle restraints: 8115 sinusoidal: 3159 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 8112 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.090 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 38.130 Find NCS groups from input model: 0.850 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.450 ------------------------------------------------------------------------------- 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 : 10.031 88.816 4905 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 % 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 *********************** 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 : 1.727 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 outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.3052 time to fit residues: 157.0892 Evaluate side-chains 174 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2607 ------------------------------------------------------------------------------- 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: 5.9990 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: 6.9990 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: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 14115 Z= 0.219 Angle : 0.634 10.193 19179 Z= 0.341 Chirality : 0.046 0.268 2187 Planarity : 0.005 0.064 2442 Dihedral : 4.853 18.361 1884 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer Outliers : 2.07 % 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: 0.97 (0.19), residues: 1704 helix: 2.37 (0.38), residues: 159 sheet: 0.54 (0.19), residues: 645 loop : 0.55 (0.20), residues: 900 *********************** 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 246 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 21 residues processed: 232 average time/residue: 0.2395 time to fit residues: 83.6295 Evaluate side-chains 204 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 1.535 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1298 time to fit residues: 7.1007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 152 optimal weight: 0.0870 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 0.0770 chunk 52 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.7918 ------------------------------------------------------------------------------- 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 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN D 551 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 14115 Z= 0.188 Angle : 0.561 9.201 19179 Z= 0.298 Chirality : 0.043 0.223 2187 Planarity : 0.004 0.038 2442 Dihedral : 4.480 16.773 1884 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 0.97 % 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: 0.83 (0.19), residues: 1704 helix: 2.72 (0.39), residues: 159 sheet: 0.42 (0.19), residues: 624 loop : 0.38 (0.20), residues: 921 *********************** 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 207 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 204 average time/residue: 0.2549 time to fit residues: 77.1899 Evaluate side-chains 174 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 1.680 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1359 time to fit residues: 3.5949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 79 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.076 14115 Z= 0.534 Angle : 0.730 9.625 19179 Z= 0.383 Chirality : 0.049 0.233 2187 Planarity : 0.006 0.061 2442 Dihedral : 4.975 27.800 1884 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 2.76 % 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: 0.13 (0.19), residues: 1704 helix: 1.40 (0.39), residues: 177 sheet: 0.17 (0.20), residues: 630 loop : -0.15 (0.19), residues: 897 *********************** 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 246 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 206 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 21 residues processed: 226 average time/residue: 0.2476 time to fit residues: 83.0103 Evaluate side-chains 204 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 1.629 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1294 time to fit residues: 7.1613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 145 optimal weight: 0.0070 chunk 40 optimal weight: 0.0010 overall best weight: 0.9006 ------------------------------------------------------------------------------- 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 41 GLN E 514 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS F 551 GLN G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14115 Z= 0.197 Angle : 0.544 9.886 19179 Z= 0.287 Chirality : 0.044 0.279 2187 Planarity : 0.004 0.032 2442 Dihedral : 4.503 23.959 1884 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer Outliers : 1.04 % 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: 1.69 (0.40), residues: 177 sheet: 0.18 (0.20), residues: 627 loop : -0.10 (0.20), residues: 900 *********************** 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 217 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 209 average time/residue: 0.2489 time to fit residues: 77.8959 Evaluate side-chains 196 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 185 time to evaluate : 1.687 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1395 time to fit residues: 5.0341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 14115 Z= 0.251 Angle : 0.553 11.375 19179 Z= 0.289 Chirality : 0.044 0.211 2187 Planarity : 0.004 0.039 2442 Dihedral : 4.426 24.867 1884 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 1.45 % 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 (0.20), residues: 1704 helix: 1.80 (0.40), residues: 177 sheet: 0.20 (0.20), residues: 612 loop : -0.16 (0.20), residues: 915 *********************** 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 207 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 198 average time/residue: 0.2540 time to fit residues: 74.9847 Evaluate side-chains 189 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 177 time to evaluate : 1.752 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1312 time to fit residues: 5.1235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 161 optimal weight: 0.0010 chunk 101 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.9792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.068 14115 Z= 0.468 Angle : 0.675 9.739 19179 Z= 0.354 Chirality : 0.048 0.261 2187 Planarity : 0.006 0.045 2442 Dihedral : 4.875 31.419 1884 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.21 (0.19), residues: 1704 helix: 1.47 (0.39), residues: 177 sheet: -0.13 (0.20), residues: 627 loop : -0.38 (0.20), residues: 900 *********************** 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 215 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 1.757 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 205 average time/residue: 0.2394 time to fit residues: 73.6126 Evaluate side-chains 191 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 182 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1320 time to fit residues: 4.1291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 31 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4845 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= 0.195 Angle : 0.545 10.317 19179 Z= 0.288 Chirality : 0.044 0.250 2187 Planarity : 0.004 0.051 2442 Dihedral : 4.552 27.817 1884 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 0.90 % 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: -0.10 (0.20), residues: 1704 helix: 1.79 (0.39), residues: 177 sheet: -0.10 (0.20), residues: 627 loop : -0.33 (0.20), residues: 900 *********************** 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 202 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 195 average time/residue: 0.2625 time to fit residues: 76.3792 Evaluate side-chains 182 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 1.710 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1235 time to fit residues: 3.3566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 150 optimal weight: 0.0040 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 118 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 136 optimal weight: 0.4980 chunk 142 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 159 optimal weight: 0.0670 overall best weight: 0.3310 ------------------------------------------------------------------------------- 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** E 551 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 14115 Z= 0.150 Angle : 0.529 12.243 19179 Z= 0.278 Chirality : 0.044 0.512 2187 Planarity : 0.004 0.033 2442 Dihedral : 4.275 24.718 1884 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 0.21 % 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: 1.58 (0.38), residues: 195 sheet: 0.26 (0.20), residues: 603 loop : -0.25 (0.20), residues: 906 *********************** 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 201 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 198 time to evaluate : 1.779 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 200 average time/residue: 0.2517 time to fit residues: 75.5535 Evaluate side-chains 187 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 1.652 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1371 time to fit residues: 2.6649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 105 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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** E 551 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 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: 0.8359 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 14115 Z= 0.371 Angle : 0.607 10.327 19179 Z= 0.321 Chirality : 0.046 0.385 2187 Planarity : 0.005 0.040 2442 Dihedral : 4.559 28.887 1884 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.41 % 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 (0.20), residues: 1704 helix: 1.51 (0.38), residues: 195 sheet: 0.05 (0.20), residues: 618 loop : -0.36 (0.20), residues: 891 ********************** 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 196 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 190 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 191 average time/residue: 0.2397 time to fit residues: 69.1643 Evaluate side-chains 188 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1341 time to fit residues: 3.0726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 117 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** E 551 GLN I 65 GLN ** 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 ** D 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.100546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.080723 restraints weight = 28992.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.080598 restraints weight = 51870.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.081187 restraints weight = 45447.580| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 14115 Z= 0.186 Angle : 0.550 11.282 19179 Z= 0.291 Chirality : 0.044 0.282 2187 Planarity : 0.004 0.031 2442 Dihedral : 4.416 26.989 1884 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.41 % 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: 0.01 (0.20), residues: 1704 helix: 1.60 (0.38), residues: 195 sheet: 0.12 (0.20), residues: 645 loop : -0.38 (0.20), residues: 864 =============================================================================== Job complete usr+sys time: 2511.55 seconds wall clock time: 46 minutes 57.80 seconds (2817.80 seconds total)