Starting phenix.real_space_refine (version: dev) on Tue Feb 21 01:28:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/02_2023/6dzm_8936.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/02_2023/6dzm_8936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/02_2023/6dzm_8936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/02_2023/6dzm_8936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/02_2023/6dzm_8936.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/02_2023/6dzm_8936.pdb" } resolution = 4.29 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= 0.003 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 Process input model Symmetric amino acids flipped Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13584 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1781 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain breaks: 3 Chain: "D" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 912 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "H" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "G" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 920 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "B" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1781 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain breaks: 3 Chain: "E" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 912 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "I" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 920 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "C" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1781 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain breaks: 3 Chain: "F" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 912 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "J" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 920 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.38, per 1000 atoms: 0.54 Number of scatterers: 13584 At special positions: 0 Unit cell: (138.86, 140.17, 111.35, 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 54 16.00 O 2649 8.00 N 2253 7.00 C 8628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS D 609 " distance=2.01 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS E 609 " distance=2.01 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS K 24 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS F 609 " distance=2.01 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " 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 N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA P 3 " - " MAN P 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 403 " - " ASN A 228 " " NAG B 403 " - " ASN B 228 " " NAG C 403 " - " ASN C 228 " " NAG D 701 " - " ASN D 618 " " NAG E 701 " - " ASN E 618 " " NAG F 701 " - " ASN F 618 " " NAG M 1 " - " ASN A 257 " " NAG N 1 " - " ASN D 563 " " NAG O 1 " - " ASN B 257 " " NAG P 1 " - " ASN E 563 " " NAG Q 1 " - " ASN C 257 " " NAG R 1 " - " ASN F 563 " Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 1.8 seconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 27 sheets defined 15.0% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 249 through 263 Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 575 removed outlier: 4.948A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'D' and resid 614 through 624 removed outlier: 4.004A pdb=" N ASN D 618 " --> pdb=" O ASP D 614 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.771A pdb=" N ALA H 85 " --> pdb=" O ASP H 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'B' and resid 78 through 85 Processing helix chain 'B' and resid 249 through 263 Processing helix chain 'E' and resid 550 through 552 No H-bonds generated for 'chain 'E' and resid 550 through 552' Processing helix chain 'E' and resid 553 through 575 removed outlier: 4.947A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA E 575 " --> pdb=" O LEU E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 Processing helix chain 'E' and resid 614 through 624 removed outlier: 4.004A pdb=" N ASN E 618 " --> pdb=" O ASP E 614 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 removed outlier: 3.770A pdb=" N ALA K 85 " --> pdb=" O ASP K 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'C' and resid 78 through 85 Processing helix chain 'C' and resid 249 through 263 Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 575 removed outlier: 4.947A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 Processing helix chain 'F' and resid 614 through 624 removed outlier: 4.005A pdb=" N ASN F 618 " --> pdb=" O ASP F 614 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.771A pdb=" N ALA L 85 " --> pdb=" O ASP L 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.603A pdb=" N GLY A 36 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 38 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 103 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 102 " --> pdb=" O TRP D 518 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.603A pdb=" N GLY A 36 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 38 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 removed outlier: 3.519A pdb=" N GLY A 87 " --> pdb=" O PHE A 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 115 removed outlier: 6.319A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N GLY A 145 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS A 114 " --> pdb=" O GLY A 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 233 through 237 removed outlier: 6.180A pdb=" N GLN A 235 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 242 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 237 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.643A pdb=" N SER H 66 " --> pdb=" O THR H 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 54 through 55 removed outlier: 6.561A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 18 through 22 Processing sheet with id=AA9, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.902A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA G 93 " --> pdb=" O SER G 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 42 through 45 removed outlier: 3.603A pdb=" N GLY B 36 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 38 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 103 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 102 " --> pdb=" O TRP E 518 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 42 through 45 removed outlier: 3.603A pdb=" N GLY B 36 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 38 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.519A pdb=" N GLY B 87 " --> pdb=" O PHE B 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 109 through 115 removed outlier: 6.319A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N GLY B 145 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS B 114 " --> pdb=" O GLY B 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 233 through 237 removed outlier: 6.180A pdb=" N GLN B 235 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B 242 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B 237 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 6 through 8 removed outlier: 3.643A pdb=" N SER K 66 " --> pdb=" O THR K 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 54 through 55 removed outlier: 6.560A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU K 34 " --> pdb=" O SER K 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 18 through 22 Processing sheet with id=AB9, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.902A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA I 93 " --> pdb=" O SER I 35 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.603A pdb=" N GLY C 36 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 38 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 103 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C 102 " --> pdb=" O TRP F 518 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.603A pdb=" N GLY C 36 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 38 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 86 through 87 removed outlier: 3.520A pdb=" N GLY C 87 " --> pdb=" O PHE C 153 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 109 through 115 removed outlier: 6.319A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N GLY C 145 " --> pdb=" O ASP C 112 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS C 114 " --> pdb=" O GLY C 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 233 through 237 removed outlier: 6.180A pdb=" N GLN C 235 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL C 242 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP C 237 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 6 through 8 removed outlier: 3.643A pdb=" N SER L 66 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.561A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N SER L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU L 34 " --> pdb=" O SER L 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 18 through 22 Processing sheet with id=AC9, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.901A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA J 93 " --> pdb=" O SER J 35 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 6.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4274 1.34 - 1.46: 3602 1.46 - 1.58: 5972 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 13914 Sorted by residual: bond pdb=" CG ASN D 618 " pdb=" ND2 ASN D 618 " ideal model delta sigma weight residual 1.328 1.367 -0.039 2.10e-02 2.27e+03 3.38e+00 bond pdb=" CG ASN E 618 " pdb=" ND2 ASN E 618 " ideal model delta sigma weight residual 1.328 1.367 -0.039 2.10e-02 2.27e+03 3.38e+00 bond pdb=" CG ASN F 618 " pdb=" ND2 ASN F 618 " ideal model delta sigma weight residual 1.328 1.367 -0.039 2.10e-02 2.27e+03 3.37e+00 bond pdb=" C1 NAG E 701 " pdb=" C2 NAG E 701 " ideal model delta sigma weight residual 1.526 1.562 -0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C1 NAG D 701 " pdb=" C2 NAG D 701 " ideal model delta sigma weight residual 1.526 1.562 -0.036 2.00e-02 2.50e+03 3.15e+00 ... (remaining 13909 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.80: 273 105.80 - 112.85: 7469 112.85 - 119.90: 4572 119.90 - 126.96: 6394 126.96 - 134.01: 222 Bond angle restraints: 18930 Sorted by residual: angle pdb=" C2 NAG M 1 " pdb=" N2 NAG M 1 " pdb=" C7 NAG M 1 " ideal model delta sigma weight residual 123.12 128.86 -5.74 1.28e+00 6.08e-01 2.00e+01 angle pdb=" C2 NAG O 1 " pdb=" N2 NAG O 1 " pdb=" C7 NAG O 1 " ideal model delta sigma weight residual 123.12 128.86 -5.74 1.28e+00 6.08e-01 2.00e+01 angle pdb=" C2 NAG Q 1 " pdb=" N2 NAG Q 1 " pdb=" C7 NAG Q 1 " ideal model delta sigma weight residual 123.12 128.86 -5.74 1.28e+00 6.08e-01 2.00e+01 angle pdb=" C ASN I 82A" pdb=" N SER I 82B" pdb=" CA SER I 82B" ideal model delta sigma weight residual 121.31 126.11 -4.80 1.49e+00 4.50e-01 1.04e+01 angle pdb=" C ASN G 82A" pdb=" N SER G 82B" pdb=" CA SER G 82B" ideal model delta sigma weight residual 121.56 126.15 -4.59 1.56e+00 4.11e-01 8.66e+00 ... (remaining 18925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 7733 15.11 - 30.21: 301 30.21 - 45.31: 72 45.31 - 60.42: 21 60.42 - 75.52: 9 Dihedral angle restraints: 8136 sinusoidal: 3291 harmonic: 4845 Sorted by residual: dihedral pdb=" CA TYR D 534 " pdb=" C TYR D 534 " pdb=" N PHE D 535 " pdb=" CA PHE D 535 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TYR E 534 " pdb=" C TYR E 534 " pdb=" N PHE E 535 " pdb=" CA PHE E 535 " ideal model delta harmonic sigma weight residual 180.00 152.09 27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TYR F 534 " pdb=" C TYR F 534 " pdb=" N PHE F 535 " pdb=" CA PHE F 535 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 8133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1545 0.047 - 0.095: 432 0.095 - 0.142: 151 0.142 - 0.190: 32 0.190 - 0.237: 6 Chirality restraints: 2166 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN E 563 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN D 563 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN F 563 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2163 not shown) Planarity restraints: 2394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 618 " -0.027 2.00e-02 2.50e+03 2.53e-02 8.03e+00 pdb=" CG ASN F 618 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN F 618 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN F 618 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG F 701 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 618 " 0.027 2.00e-02 2.50e+03 2.52e-02 7.96e+00 pdb=" CG ASN D 618 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN D 618 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN D 618 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG D 701 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 618 " -0.027 2.00e-02 2.50e+03 2.51e-02 7.87e+00 pdb=" CG ASN E 618 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN E 618 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN E 618 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG E 701 " -0.029 2.00e-02 2.50e+03 ... (remaining 2391 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 312 2.63 - 3.19: 13107 3.19 - 3.76: 21029 3.76 - 4.33: 29430 4.33 - 4.90: 46464 Nonbonded interactions: 110342 Sorted by model distance: nonbonded pdb=" O4 NAG N 1 " pdb=" O7 NAG N 2 " model vdw 2.058 2.440 nonbonded pdb=" O4 NAG R 1 " pdb=" O7 NAG R 2 " model vdw 2.058 2.440 nonbonded pdb=" O4 NAG P 1 " pdb=" O7 NAG P 2 " model vdw 2.058 2.440 nonbonded pdb=" O3 NAG P 2 " pdb=" O5 BMA P 3 " model vdw 2.203 2.440 nonbonded pdb=" O3 NAG R 2 " pdb=" O5 BMA R 3 " model vdw 2.203 2.440 ... (remaining 110337 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 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8628 2.51 5 N 2253 2.21 5 O 2649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.920 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: 8.220 Check model and map are aligned: 0.220 Process input model: 35.240 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.008 0.065 13914 Z= 0.503 Angle : 0.910 7.197 18930 Z= 0.494 Chirality : 0.052 0.237 2166 Planarity : 0.006 0.049 2382 Dihedral : 9.656 75.524 4977 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.61 % Favored : 86.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -4.76 (0.18), residues: 1653 helix: -2.49 (0.28), residues: 207 sheet: -3.57 (0.19), residues: 441 loop : -3.23 (0.18), residues: 1005 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 325 average time/residue: 0.4129 time to fit residues: 171.0434 Evaluate side-chains 136 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.635 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 84 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 96 optimal weight: 0.4980 chunk 149 optimal weight: 0.0470 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 224 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN C 44 GLN C 224 ASN F 567 GLN ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 13914 Z= 0.222 Angle : 0.751 13.585 18930 Z= 0.397 Chirality : 0.050 0.408 2166 Planarity : 0.006 0.052 2382 Dihedral : 7.675 85.383 2025 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -3.67 (0.19), residues: 1653 helix: -1.19 (0.32), residues: 213 sheet: -3.00 (0.19), residues: 453 loop : -2.49 (0.20), residues: 987 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 243 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 247 average time/residue: 0.3215 time to fit residues: 108.0615 Evaluate side-chains 121 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 120 optimal weight: 0.3980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 224 ASN ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 HIS ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 13914 Z= 0.427 Angle : 0.831 12.612 18930 Z= 0.434 Chirality : 0.051 0.493 2166 Planarity : 0.006 0.057 2382 Dihedral : 7.553 85.890 2025 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.41 % Favored : 89.53 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -3.23 (0.19), residues: 1653 helix: -0.77 (0.32), residues: 210 sheet: -2.40 (0.19), residues: 486 loop : -2.36 (0.20), residues: 957 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.3104 time to fit residues: 74.3094 Evaluate side-chains 97 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.724 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 10.0000 chunk 112 optimal weight: 0.0970 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 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 38 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN E 560 GLN C 39 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 GLN F 570 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 13914 Z= 0.248 Angle : 0.662 6.660 18930 Z= 0.350 Chirality : 0.047 0.376 2166 Planarity : 0.005 0.062 2382 Dihedral : 7.130 84.853 2025 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.80 (0.20), residues: 1653 helix: -0.29 (0.33), residues: 213 sheet: -2.04 (0.20), residues: 489 loop : -2.16 (0.21), residues: 951 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.3168 time to fit residues: 77.1421 Evaluate side-chains 108 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 GLN H 80 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS J 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.065 13914 Z= 0.450 Angle : 0.792 11.659 18930 Z= 0.415 Chirality : 0.048 0.382 2166 Planarity : 0.006 0.055 2382 Dihedral : 7.225 81.673 2025 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.62 (0.20), residues: 1653 helix: -0.35 (0.32), residues: 210 sheet: -1.71 (0.22), residues: 489 loop : -2.12 (0.21), residues: 954 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.3051 time to fit residues: 65.7325 Evaluate side-chains 95 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.538 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 13914 Z= 0.302 Angle : 0.676 8.438 18930 Z= 0.358 Chirality : 0.047 0.381 2166 Planarity : 0.005 0.062 2382 Dihedral : 6.972 82.294 2025 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.40 (0.21), residues: 1653 helix: -0.27 (0.32), residues: 213 sheet: -1.63 (0.22), residues: 504 loop : -1.90 (0.22), residues: 936 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3225 time to fit residues: 70.5722 Evaluate side-chains 98 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.720 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 134 optimal weight: 0.1980 chunk 89 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 13914 Z= 0.182 Angle : 0.632 6.525 18930 Z= 0.332 Chirality : 0.046 0.366 2166 Planarity : 0.005 0.055 2382 Dihedral : 6.636 84.681 2025 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.18 (0.21), residues: 1653 helix: -0.04 (0.33), residues: 213 sheet: -1.45 (0.22), residues: 510 loop : -1.79 (0.22), residues: 930 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.3287 time to fit residues: 77.3509 Evaluate side-chains 111 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN F 521 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.054 13914 Z= 0.441 Angle : 0.753 7.620 18930 Z= 0.400 Chirality : 0.048 0.407 2166 Planarity : 0.005 0.059 2382 Dihedral : 6.782 80.997 2025 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.32 (0.21), residues: 1653 helix: -0.22 (0.31), residues: 210 sheet: -1.61 (0.22), residues: 501 loop : -1.82 (0.22), residues: 942 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 137 average time/residue: 0.3116 time to fit residues: 60.0950 Evaluate side-chains 98 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1615 time to fit residues: 2.3368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.4980 chunk 139 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 0.0030 chunk 45 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 97 optimal weight: 0.0980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 13914 Z= 0.183 Angle : 0.642 7.034 18930 Z= 0.338 Chirality : 0.047 0.375 2166 Planarity : 0.005 0.054 2382 Dihedral : 6.575 83.760 2025 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.01 (0.21), residues: 1653 helix: 0.18 (0.34), residues: 210 sheet: -1.31 (0.23), residues: 474 loop : -1.72 (0.21), residues: 969 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.3189 time to fit residues: 77.8302 Evaluate side-chains 108 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 13914 Z= 0.197 Angle : 0.638 6.909 18930 Z= 0.337 Chirality : 0.046 0.382 2166 Planarity : 0.005 0.057 2382 Dihedral : 6.436 84.218 2025 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.91 (0.21), residues: 1653 helix: 0.09 (0.33), residues: 210 sheet: -1.19 (0.23), residues: 498 loop : -1.63 (0.22), residues: 945 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.3149 time to fit residues: 73.4384 Evaluate side-chains 109 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.688 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.042585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.034682 restraints weight = 114863.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.035717 restraints weight = 72769.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.036252 restraints weight = 52296.888| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 13914 Z= 0.197 Angle : 0.629 7.299 18930 Z= 0.333 Chirality : 0.046 0.385 2166 Planarity : 0.005 0.055 2382 Dihedral : 6.352 83.654 2025 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.81 (0.21), residues: 1653 helix: 0.10 (0.33), residues: 210 sheet: -1.08 (0.23), residues: 498 loop : -1.58 (0.22), residues: 945 =============================================================================== Job complete usr+sys time: 2589.91 seconds wall clock time: 48 minutes 5.64 seconds (2885.64 seconds total)