Starting phenix.real_space_refine on Thu Feb 15 22:20:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/02_2024/6dzm_8936.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/02_2024/6dzm_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_2024/6dzm_8936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/02_2024/6dzm_8936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/02_2024/6dzm_8936.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/02_2024/6dzm_8936.pdb" } resolution = 4.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 dihedrals: 6 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: 15 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 dihedrals: 6 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: 15 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 dihedrals: 6 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: 15 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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: 5.76 Conformation dependent library (CDL) restraints added in 2.5 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: 1.44 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: 3.77 Time building geometry restraints manager: 6.22 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=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.23e+00 bond pdb=" C1 NAG F 701 " pdb=" O5 NAG F 701 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" C1 NAG E 701 " pdb=" O5 NAG E 701 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.21e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.32e+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=" 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 angle pdb=" C ASN J 82A" pdb=" N SER J 82B" pdb=" CA SER J 82B" ideal model delta sigma weight residual 121.56 126.13 -4.57 1.56e+00 4.11e-01 8.59e+00 angle pdb=" N GLY F 528 " pdb=" CA GLY F 528 " pdb=" C GLY F 528 " ideal model delta sigma weight residual 113.18 106.49 6.69 2.37e+00 1.78e-01 7.98e+00 angle pdb=" N GLY D 528 " pdb=" CA GLY D 528 " pdb=" C GLY D 528 " ideal model delta sigma weight residual 113.18 106.50 6.68 2.37e+00 1.78e-01 7.95e+00 ... (remaining 18925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 8222 23.20 - 46.39: 178 46.39 - 69.59: 51 69.59 - 92.79: 24 92.79 - 115.98: 12 Dihedral angle restraints: 8487 sinusoidal: 3642 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 8484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1512 0.047 - 0.095: 441 0.095 - 0.142: 175 0.142 - 0.190: 29 0.190 - 0.237: 9 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 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: 2.400 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: 7.720 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 37.680 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.130 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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= 0.519 Angle : 0.956 7.197 18930 Z= 0.494 Chirality : 0.054 0.237 2166 Planarity : 0.006 0.049 2382 Dihedral : 12.552 115.981 5328 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 % Allowed : 1.26 % Favored : 98.74 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP F 597 HIS 0.009 0.003 HIS F 516 PHE 0.027 0.003 PHE A 160 TYR 0.025 0.002 TYR L 92 ARG 0.009 0.001 ARG C 85 *********************** 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 : 1.723 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 REVERT: A 33 ILE cc_start: 0.8833 (mt) cc_final: 0.8317 (mm) REVERT: A 39 HIS cc_start: 0.8481 (t70) cc_final: 0.8189 (t70) REVERT: A 163 ASP cc_start: 0.8933 (t0) cc_final: 0.7782 (t0) REVERT: D 567 GLN cc_start: 0.9319 (tt0) cc_final: 0.8815 (tt0) REVERT: D 588 LYS cc_start: 0.9030 (tppt) cc_final: 0.8731 (tttm) REVERT: D 591 ASP cc_start: 0.8806 (m-30) cc_final: 0.8499 (m-30) REVERT: H 87 TYR cc_start: 0.8474 (m-10) cc_final: 0.8196 (m-10) REVERT: H 103 LYS cc_start: 0.9478 (tptm) cc_final: 0.9223 (tppt) REVERT: G 32 TYR cc_start: 0.8878 (m-80) cc_final: 0.7951 (m-80) REVERT: B 33 ILE cc_start: 0.8871 (mt) cc_final: 0.8325 (mm) REVERT: B 162 TYR cc_start: 0.8707 (m-80) cc_final: 0.8487 (m-10) REVERT: B 163 ASP cc_start: 0.8864 (t0) cc_final: 0.8005 (t0) REVERT: E 588 LYS cc_start: 0.9165 (tppt) cc_final: 0.8942 (tttp) REVERT: E 591 ASP cc_start: 0.8765 (m-30) cc_final: 0.8294 (m-30) REVERT: C 33 ILE cc_start: 0.8816 (mt) cc_final: 0.8153 (mt) REVERT: C 163 ASP cc_start: 0.8743 (t0) cc_final: 0.7269 (t0) REVERT: F 567 GLN cc_start: 0.9316 (tt0) cc_final: 0.8979 (tt0) REVERT: F 588 LYS cc_start: 0.9110 (tppt) cc_final: 0.8805 (tttp) REVERT: F 591 ASP cc_start: 0.8967 (m-30) cc_final: 0.8646 (m-30) REVERT: L 87 TYR cc_start: 0.8412 (m-10) cc_final: 0.8194 (m-10) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.4117 time to fit residues: 170.2621 Evaluate side-chains 144 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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: 0.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 149 optimal weight: 8.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13914 Z= 0.218 Angle : 0.780 13.715 18930 Z= 0.389 Chirality : 0.049 0.246 2166 Planarity : 0.006 0.054 2382 Dihedral : 12.148 85.560 2376 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.28 % Allowed : 1.33 % Favored : 98.39 % 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: -3.69 (0.19), residues: 1653 helix: -1.04 (0.33), residues: 213 sheet: -3.03 (0.18), residues: 459 loop : -2.53 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP J 103 HIS 0.005 0.001 HIS J 100D PHE 0.015 0.002 PHE J 67 TYR 0.021 0.002 TYR G 79 ARG 0.006 0.001 ARG A 54 *********************** 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 243 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 239 time to evaluate : 1.540 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: A 33 ILE cc_start: 0.9052 (mt) cc_final: 0.8756 (mm) REVERT: A 49 ASP cc_start: 0.8802 (p0) cc_final: 0.8467 (p0) REVERT: A 163 ASP cc_start: 0.9069 (t0) cc_final: 0.8354 (t0) REVERT: D 567 GLN cc_start: 0.9378 (tt0) cc_final: 0.8749 (tm-30) REVERT: D 571 LEU cc_start: 0.9376 (mt) cc_final: 0.8938 (mt) REVERT: D 591 ASP cc_start: 0.8867 (m-30) cc_final: 0.8495 (m-30) REVERT: D 602 HIS cc_start: 0.8960 (m-70) cc_final: 0.8738 (t70) REVERT: H 87 TYR cc_start: 0.8427 (m-10) cc_final: 0.8109 (m-80) REVERT: G 82 MET cc_start: 0.8604 (mmm) cc_final: 0.8338 (mmm) REVERT: B 33 ILE cc_start: 0.8987 (mt) cc_final: 0.8744 (mm) REVERT: B 49 ASP cc_start: 0.8736 (p0) cc_final: 0.8371 (p0) REVERT: B 163 ASP cc_start: 0.9084 (t0) cc_final: 0.8674 (t0) REVERT: E 584 ILE cc_start: 0.8921 (pt) cc_final: 0.8684 (mp) REVERT: E 587 ARG cc_start: 0.8942 (mtp-110) cc_final: 0.8662 (mtp-110) REVERT: E 591 ASP cc_start: 0.8845 (m-30) cc_final: 0.8471 (m-30) REVERT: E 618 ASN cc_start: 0.6541 (p0) cc_final: 0.5783 (t0) REVERT: K 87 TYR cc_start: 0.8494 (m-80) cc_final: 0.8160 (m-10) REVERT: I 67 PHE cc_start: 0.8738 (m-80) cc_final: 0.8373 (m-10) REVERT: I 80 LEU cc_start: 0.9781 (tp) cc_final: 0.9280 (tp) REVERT: C 33 ILE cc_start: 0.9051 (mt) cc_final: 0.8708 (mt) REVERT: C 49 ASP cc_start: 0.8972 (p0) cc_final: 0.8526 (p0) REVERT: C 163 ASP cc_start: 0.8768 (t0) cc_final: 0.8532 (t0) REVERT: F 567 GLN cc_start: 0.9331 (tt0) cc_final: 0.8832 (tt0) REVERT: F 587 ARG cc_start: 0.8928 (mtp-110) cc_final: 0.8649 (mtp-110) REVERT: F 591 ASP cc_start: 0.8988 (m-30) cc_final: 0.8555 (m-30) REVERT: L 33 TRP cc_start: 0.7365 (m-10) cc_final: 0.7006 (m-10) REVERT: L 87 TYR cc_start: 0.8303 (m-10) cc_final: 0.7773 (m-10) outliers start: 4 outliers final: 0 residues processed: 243 average time/residue: 0.3269 time to fit residues: 108.0149 Evaluate side-chains 132 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.637 ------------------------------------------------------------------------------- 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: 0.2980 chunk 46 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 133 optimal weight: 0.0040 chunk 148 optimal weight: 0.0570 chunk 51 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.5912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS D 595 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13914 Z= 0.190 Angle : 0.696 9.929 18930 Z= 0.343 Chirality : 0.047 0.293 2166 Planarity : 0.005 0.053 2382 Dihedral : 10.450 87.745 2376 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.14 % Allowed : 1.26 % Favored : 98.60 % 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: -3.12 (0.20), residues: 1653 helix: -0.17 (0.35), residues: 213 sheet: -2.59 (0.19), residues: 471 loop : -2.29 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 103 HIS 0.005 0.001 HIS J 100D PHE 0.012 0.001 PHE D 592 TYR 0.016 0.001 TYR A 261 ARG 0.006 0.001 ARG I 97 *********************** 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 202 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 200 time to evaluate : 1.433 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: D 587 ARG cc_start: 0.8906 (mtp-110) cc_final: 0.8223 (ttp80) REVERT: D 591 ASP cc_start: 0.8932 (m-30) cc_final: 0.8267 (m-30) REVERT: H 46 LYS cc_start: 0.9166 (ptmt) cc_final: 0.8715 (ptmm) REVERT: H 87 TYR cc_start: 0.8467 (m-10) cc_final: 0.8126 (m-80) REVERT: G 45 LEU cc_start: 0.8868 (mm) cc_final: 0.8595 (mm) REVERT: B 33 ILE cc_start: 0.8724 (mt) cc_final: 0.8275 (mm) REVERT: B 49 ASP cc_start: 0.8593 (p0) cc_final: 0.8359 (p0) REVERT: B 100 GLU cc_start: 0.7525 (pp20) cc_final: 0.7301 (pp20) REVERT: B 163 ASP cc_start: 0.9000 (t0) cc_final: 0.8731 (t0) REVERT: B 170 ILE cc_start: 0.9309 (mp) cc_final: 0.9012 (mm) REVERT: E 584 ILE cc_start: 0.9067 (pt) cc_final: 0.8815 (mp) REVERT: E 587 ARG cc_start: 0.8927 (mtp-110) cc_final: 0.8235 (ttp80) REVERT: E 591 ASP cc_start: 0.9067 (m-30) cc_final: 0.8320 (m-30) REVERT: K 87 TYR cc_start: 0.8659 (m-80) cc_final: 0.8298 (m-10) REVERT: I 79 TYR cc_start: 0.8792 (m-10) cc_final: 0.8497 (m-80) REVERT: C 33 ILE cc_start: 0.8902 (mt) cc_final: 0.8290 (mt) REVERT: C 49 ASP cc_start: 0.8509 (p0) cc_final: 0.8233 (p0) REVERT: F 548 MET cc_start: 0.8802 (mtp) cc_final: 0.8330 (tpp) REVERT: F 567 GLN cc_start: 0.9395 (tt0) cc_final: 0.8931 (tm-30) REVERT: F 571 LEU cc_start: 0.9320 (mt) cc_final: 0.8805 (mt) REVERT: F 587 ARG cc_start: 0.8906 (mtp-110) cc_final: 0.8692 (mtp-110) REVERT: F 588 LYS cc_start: 0.9188 (tppt) cc_final: 0.8836 (tttm) REVERT: F 591 ASP cc_start: 0.9107 (m-30) cc_final: 0.8691 (m-30) REVERT: L 33 TRP cc_start: 0.7530 (m-10) cc_final: 0.7009 (m-10) REVERT: L 87 TYR cc_start: 0.8424 (m-10) cc_final: 0.7806 (m-10) REVERT: J 32 TYR cc_start: 0.8999 (m-80) cc_final: 0.8746 (m-80) REVERT: J 79 TYR cc_start: 0.8771 (m-80) cc_final: 0.8133 (m-80) outliers start: 2 outliers final: 0 residues processed: 202 average time/residue: 0.2951 time to fit residues: 82.8187 Evaluate side-chains 127 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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: 0.0470 chunk 112 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 142 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** D 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN H 39 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13914 Z= 0.167 Angle : 0.659 9.325 18930 Z= 0.325 Chirality : 0.045 0.242 2166 Planarity : 0.005 0.044 2382 Dihedral : 9.268 89.756 2376 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.35 % Allowed : 1.61 % Favored : 98.04 % 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: -2.79 (0.20), residues: 1653 helix: 0.13 (0.35), residues: 213 sheet: -2.33 (0.19), residues: 486 loop : -2.08 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 86 HIS 0.005 0.001 HIS I 100D PHE 0.011 0.001 PHE D 592 TYR 0.016 0.001 TYR B 171 ARG 0.005 0.001 ARG J 38 *********************** 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 207 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 202 time to evaluate : 1.655 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: A 33 ILE cc_start: 0.8746 (mm) cc_final: 0.8473 (mm) REVERT: A 163 ASP cc_start: 0.8764 (t70) cc_final: 0.8482 (t70) REVERT: D 587 ARG cc_start: 0.8938 (mtp-110) cc_final: 0.8323 (ttp80) REVERT: D 588 LYS cc_start: 0.9189 (tppt) cc_final: 0.8952 (tttt) REVERT: D 591 ASP cc_start: 0.9014 (m-30) cc_final: 0.8406 (m-30) REVERT: D 617 LYS cc_start: 0.9203 (mmpt) cc_final: 0.8977 (mmtm) REVERT: G 45 LEU cc_start: 0.8899 (mm) cc_final: 0.8594 (mm) REVERT: G 67 PHE cc_start: 0.8002 (m-80) cc_final: 0.7708 (m-80) REVERT: B 253 LEU cc_start: 0.9387 (mt) cc_final: 0.9170 (tt) REVERT: E 584 ILE cc_start: 0.9139 (pt) cc_final: 0.8875 (mp) REVERT: E 587 ARG cc_start: 0.8768 (mtp-110) cc_final: 0.8248 (ttp80) REVERT: E 591 ASP cc_start: 0.9036 (m-30) cc_final: 0.8207 (m-30) REVERT: E 618 ASN cc_start: 0.7286 (p0) cc_final: 0.7050 (p0) REVERT: K 87 TYR cc_start: 0.8567 (m-80) cc_final: 0.8214 (m-10) REVERT: I 79 TYR cc_start: 0.8627 (m-10) cc_final: 0.8379 (m-10) REVERT: C 33 ILE cc_start: 0.8873 (mt) cc_final: 0.8628 (mm) REVERT: C 163 ASP cc_start: 0.8811 (t70) cc_final: 0.8361 (t0) REVERT: C 164 ARG cc_start: 0.9233 (ttm110) cc_final: 0.8779 (mtm-85) REVERT: F 548 MET cc_start: 0.8856 (mtp) cc_final: 0.8386 (tpp) REVERT: F 567 GLN cc_start: 0.9380 (tt0) cc_final: 0.9027 (tt0) REVERT: F 587 ARG cc_start: 0.8935 (mtp-110) cc_final: 0.8681 (mtp-110) REVERT: F 591 ASP cc_start: 0.9213 (m-30) cc_final: 0.8758 (m-30) REVERT: L 33 TRP cc_start: 0.7586 (m-10) cc_final: 0.7016 (m-10) REVERT: L 87 TYR cc_start: 0.8373 (m-10) cc_final: 0.7698 (m-10) REVERT: J 45 LEU cc_start: 0.8828 (mm) cc_final: 0.8443 (mm) REVERT: J 79 TYR cc_start: 0.8720 (m-80) cc_final: 0.8128 (m-80) outliers start: 5 outliers final: 1 residues processed: 207 average time/residue: 0.3047 time to fit residues: 87.8643 Evaluate side-chains 137 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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: 3.9990 chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 GLN ** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 13914 Z= 0.565 Angle : 0.990 9.974 18930 Z= 0.494 Chirality : 0.055 0.330 2166 Planarity : 0.007 0.066 2382 Dihedral : 9.568 79.548 2376 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 28.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.68 % Favored : 88.26 % Rotamer: Outliers : 0.21 % Allowed : 3.22 % Favored : 96.57 % 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: -2.85 (0.20), residues: 1653 helix: -0.51 (0.32), residues: 213 sheet: -2.00 (0.20), residues: 495 loop : -2.19 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP C 86 HIS 0.010 0.003 HIS E 516 PHE 0.029 0.003 PHE G 100E TYR 0.033 0.004 TYR K 87 ARG 0.022 0.001 ARG A 85 *********************** 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 145 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 587 ARG cc_start: 0.9225 (mtp-110) cc_final: 0.8814 (mtp-110) REVERT: D 591 ASP cc_start: 0.9423 (m-30) cc_final: 0.8789 (m-30) REVERT: H 46 LYS cc_start: 0.9180 (pttm) cc_final: 0.8869 (pttm) REVERT: B 47 ASP cc_start: 0.8602 (t0) cc_final: 0.8393 (t0) REVERT: B 49 ASP cc_start: 0.8641 (p0) cc_final: 0.8392 (p0) REVERT: B 253 LEU cc_start: 0.9464 (mt) cc_final: 0.9199 (tt) REVERT: E 591 ASP cc_start: 0.9418 (m-30) cc_final: 0.9009 (m-30) REVERT: E 618 ASN cc_start: 0.7826 (p0) cc_final: 0.7530 (p0) REVERT: K 46 LYS cc_start: 0.9382 (ptmt) cc_final: 0.8990 (ptmm) REVERT: I 79 TYR cc_start: 0.8810 (m-10) cc_final: 0.8521 (m-80) REVERT: I 82 MET cc_start: 0.8912 (mmp) cc_final: 0.8689 (mmp) REVERT: C 49 ASP cc_start: 0.8608 (p0) cc_final: 0.8316 (p0) REVERT: C 164 ARG cc_start: 0.9376 (ttm110) cc_final: 0.8947 (ttp-170) REVERT: J 34 MET cc_start: 0.8800 (mmt) cc_final: 0.8584 (mmm) REVERT: J 79 TYR cc_start: 0.8850 (m-80) cc_final: 0.8452 (m-10) outliers start: 3 outliers final: 1 residues processed: 144 average time/residue: 0.3219 time to fit residues: 64.3400 Evaluate side-chains 97 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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: 0.8980 chunk 143 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 GLN ** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 HIS H 39 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 13914 Z= 0.212 Angle : 0.690 9.197 18930 Z= 0.344 Chirality : 0.047 0.284 2166 Planarity : 0.005 0.042 2382 Dihedral : 8.765 84.751 2376 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.07 % Allowed : 1.12 % Favored : 98.81 % 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: -2.34 (0.21), residues: 1653 helix: -0.12 (0.34), residues: 210 sheet: -1.51 (0.23), residues: 459 loop : -1.94 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 86 HIS 0.003 0.001 HIS G 100D PHE 0.018 0.002 PHE G 67 TYR 0.021 0.002 TYR K 88 ARG 0.005 0.001 ARG B 89 *********************** 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 175 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.629 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: A 49 ASP cc_start: 0.8900 (p0) cc_final: 0.8628 (p0) REVERT: A 253 LEU cc_start: 0.9532 (mt) cc_final: 0.9232 (tt) REVERT: D 587 ARG cc_start: 0.9057 (mtp-110) cc_final: 0.8714 (mtp85) REVERT: D 591 ASP cc_start: 0.9328 (m-30) cc_final: 0.8866 (m-30) REVERT: H 39 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7734 (pp30) REVERT: B 253 LEU cc_start: 0.9449 (mt) cc_final: 0.9174 (tt) REVERT: E 618 ASN cc_start: 0.7778 (p0) cc_final: 0.7536 (p0) REVERT: I 79 TYR cc_start: 0.8680 (m-10) cc_final: 0.8382 (m-80) REVERT: C 49 ASP cc_start: 0.8391 (p0) cc_final: 0.8059 (p0) REVERT: C 164 ARG cc_start: 0.9238 (ttm110) cc_final: 0.8823 (ttp-110) REVERT: C 253 LEU cc_start: 0.9440 (mt) cc_final: 0.9122 (tt) REVERT: F 587 ARG cc_start: 0.9140 (mtp-110) cc_final: 0.8847 (mtp-110) REVERT: F 591 ASP cc_start: 0.9372 (m-30) cc_final: 0.8952 (m-30) REVERT: J 34 MET cc_start: 0.8726 (mmt) cc_final: 0.8496 (mmm) REVERT: J 45 LEU cc_start: 0.8901 (mm) cc_final: 0.8564 (mm) REVERT: J 79 TYR cc_start: 0.8808 (m-80) cc_final: 0.8399 (m-80) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.3435 time to fit residues: 82.7951 Evaluate side-chains 115 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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: 4.9990 chunk 17 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 521 GLN ** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13914 Z= 0.260 Angle : 0.679 9.193 18930 Z= 0.340 Chirality : 0.046 0.245 2166 Planarity : 0.005 0.053 2382 Dihedral : 8.478 84.654 2376 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 0.07 % Allowed : 1.40 % Favored : 98.53 % 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: -2.12 (0.21), residues: 1653 helix: 0.05 (0.33), residues: 210 sheet: -1.43 (0.22), residues: 507 loop : -1.75 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 86 HIS 0.003 0.001 HIS D 602 PHE 0.016 0.002 PHE G 29 TYR 0.023 0.002 TYR K 88 ARG 0.010 0.001 ARG E 587 *********************** 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 152 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.740 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: A 49 ASP cc_start: 0.8645 (p0) cc_final: 0.8380 (p0) REVERT: A 253 LEU cc_start: 0.9533 (mt) cc_final: 0.9219 (tt) REVERT: B 253 LEU cc_start: 0.9442 (mt) cc_final: 0.9162 (tt) REVERT: E 540 GLU cc_start: 0.7707 (tp30) cc_final: 0.7489 (tp30) REVERT: E 587 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7094 (ttp80) REVERT: E 591 ASP cc_start: 0.9172 (m-30) cc_final: 0.8428 (m-30) REVERT: E 618 ASN cc_start: 0.7823 (p0) cc_final: 0.7525 (p0) REVERT: I 79 TYR cc_start: 0.8657 (m-10) cc_final: 0.8330 (m-80) REVERT: C 49 ASP cc_start: 0.8290 (p0) cc_final: 0.8055 (p0) REVERT: C 253 LEU cc_start: 0.9383 (mt) cc_final: 0.9075 (tt) REVERT: F 587 ARG cc_start: 0.9040 (mtp-110) cc_final: 0.8452 (ttp80) REVERT: F 591 ASP cc_start: 0.9373 (m-30) cc_final: 0.8745 (m-30) REVERT: J 34 MET cc_start: 0.8755 (mmt) cc_final: 0.8533 (mmm) REVERT: J 45 LEU cc_start: 0.8844 (mm) cc_final: 0.8572 (mm) REVERT: J 79 TYR cc_start: 0.8880 (m-80) cc_final: 0.8455 (m-80) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.3316 time to fit residues: 69.4674 Evaluate side-chains 107 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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: 6.9990 chunk 94 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 chunk 78 optimal weight: 0.0770 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 521 GLN D 560 GLN H 39 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 GLN E 570 GLN ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13914 Z= 0.164 Angle : 0.641 9.355 18930 Z= 0.319 Chirality : 0.045 0.218 2166 Planarity : 0.004 0.046 2382 Dihedral : 8.043 85.894 2376 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.07 % Allowed : 1.33 % Favored : 98.60 % 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: -1.99 (0.21), residues: 1653 helix: 0.04 (0.34), residues: 213 sheet: -1.28 (0.24), residues: 441 loop : -1.68 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 86 HIS 0.003 0.001 HIS D 602 PHE 0.018 0.002 PHE G 29 TYR 0.025 0.001 TYR K 88 ARG 0.009 0.001 ARG F 587 *********************** 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 167 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.632 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: A 130 ARG cc_start: 0.8756 (mpp80) cc_final: 0.8414 (mpp80) REVERT: A 163 ASP cc_start: 0.9015 (t70) cc_final: 0.8597 (t0) REVERT: A 253 LEU cc_start: 0.9463 (mt) cc_final: 0.9142 (tt) REVERT: G 32 TYR cc_start: 0.8643 (m-80) cc_final: 0.8173 (m-80) REVERT: B 49 ASP cc_start: 0.8753 (p0) cc_final: 0.8504 (p0) REVERT: B 163 ASP cc_start: 0.9184 (t70) cc_final: 0.8975 (t0) REVERT: B 253 LEU cc_start: 0.9426 (mt) cc_final: 0.9177 (tt) REVERT: E 540 GLU cc_start: 0.7680 (tp30) cc_final: 0.7465 (tp30) REVERT: E 618 ASN cc_start: 0.7758 (p0) cc_final: 0.7453 (p0) REVERT: I 79 TYR cc_start: 0.8615 (m-10) cc_final: 0.8339 (m-80) REVERT: I 82 MET cc_start: 0.8695 (mmp) cc_final: 0.8388 (mmp) REVERT: C 253 LEU cc_start: 0.9345 (mt) cc_final: 0.9013 (tt) REVERT: F 615 TRP cc_start: 0.6962 (t-100) cc_final: 0.6426 (t-100) REVERT: J 34 MET cc_start: 0.8686 (mmt) cc_final: 0.8469 (mmm) REVERT: J 45 LEU cc_start: 0.8754 (mm) cc_final: 0.8288 (mm) REVERT: J 79 TYR cc_start: 0.8757 (m-80) cc_final: 0.8406 (m-10) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.3358 time to fit residues: 77.0918 Evaluate side-chains 116 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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: 5.9990 chunk 139 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 0.0370 chunk 97 optimal weight: 1.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 521 GLN H 39 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13914 Z= 0.225 Angle : 0.647 9.349 18930 Z= 0.323 Chirality : 0.045 0.217 2166 Planarity : 0.005 0.047 2382 Dihedral : 7.934 84.318 2376 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 0.14 % Allowed : 0.56 % Favored : 99.30 % 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: -1.85 (0.21), residues: 1653 helix: 0.12 (0.34), residues: 213 sheet: -1.13 (0.24), residues: 444 loop : -1.61 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 86 HIS 0.003 0.001 HIS F 516 PHE 0.030 0.002 PHE J 100E TYR 0.026 0.002 TYR K 88 ARG 0.010 0.001 ARG G 66 *********************** 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 156 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.450 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: A 99 TYR cc_start: 0.8344 (p90) cc_final: 0.8110 (p90) REVERT: A 163 ASP cc_start: 0.9059 (t70) cc_final: 0.8766 (t0) REVERT: A 253 LEU cc_start: 0.9496 (mt) cc_final: 0.9177 (tt) REVERT: D 587 ARG cc_start: 0.8568 (ttp80) cc_final: 0.7438 (ttp80) REVERT: D 591 ASP cc_start: 0.9431 (t0) cc_final: 0.9195 (m-30) REVERT: G 32 TYR cc_start: 0.8741 (m-80) cc_final: 0.8482 (m-10) REVERT: B 49 ASP cc_start: 0.8634 (p0) cc_final: 0.8400 (p0) REVERT: B 253 LEU cc_start: 0.9420 (mt) cc_final: 0.9175 (tt) REVERT: E 540 GLU cc_start: 0.7712 (tp30) cc_final: 0.7467 (tp30) REVERT: E 618 ASN cc_start: 0.7792 (p0) cc_final: 0.7477 (p0) REVERT: I 79 TYR cc_start: 0.8695 (m-10) cc_final: 0.8266 (m-80) REVERT: I 80 LEU cc_start: 0.9729 (tp) cc_final: 0.9467 (tp) REVERT: C 253 LEU cc_start: 0.9337 (mt) cc_final: 0.8997 (tt) REVERT: F 615 TRP cc_start: 0.7235 (t-100) cc_final: 0.6642 (t-100) REVERT: J 79 TYR cc_start: 0.8840 (m-80) cc_final: 0.8468 (m-80) outliers start: 2 outliers final: 1 residues processed: 156 average time/residue: 0.3151 time to fit residues: 67.9588 Evaluate side-chains 112 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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: 8.9990 chunk 95 optimal weight: 0.0970 chunk 74 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 164 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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** H 39 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13914 Z= 0.165 Angle : 0.641 9.407 18930 Z= 0.319 Chirality : 0.045 0.219 2166 Planarity : 0.005 0.059 2382 Dihedral : 7.739 84.733 2376 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % 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: -1.71 (0.21), residues: 1653 helix: 0.20 (0.34), residues: 213 sheet: -0.94 (0.24), residues: 435 loop : -1.56 (0.21), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 86 HIS 0.003 0.001 HIS J 100D PHE 0.022 0.002 PHE I 67 TYR 0.022 0.001 TYR K 88 ARG 0.008 0.001 ARG F 587 ********************** 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 152 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.467 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: A 99 TYR cc_start: 0.8258 (p90) cc_final: 0.8003 (p90) REVERT: A 163 ASP cc_start: 0.8863 (t70) cc_final: 0.8517 (t0) REVERT: A 253 LEU cc_start: 0.9431 (mt) cc_final: 0.9208 (tt) REVERT: D 587 ARG cc_start: 0.8498 (ttp80) cc_final: 0.7924 (ttp80) REVERT: G 103 TRP cc_start: 0.8652 (m100) cc_final: 0.8448 (m100) REVERT: B 253 LEU cc_start: 0.9416 (mt) cc_final: 0.9185 (tt) REVERT: E 587 ARG cc_start: 0.8646 (ttp80) cc_final: 0.7685 (ttp80) REVERT: E 618 ASN cc_start: 0.7681 (p0) cc_final: 0.7366 (p0) REVERT: C 49 ASP cc_start: 0.8488 (p0) cc_final: 0.8247 (p0) REVERT: C 253 LEU cc_start: 0.9340 (mt) cc_final: 0.8918 (tt) REVERT: F 615 TRP cc_start: 0.7086 (t-100) cc_final: 0.6589 (t-100) REVERT: J 79 TYR cc_start: 0.8825 (m-80) cc_final: 0.8227 (m-10) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.2838 time to fit residues: 61.9438 Evaluate side-chains 112 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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: 0.9990 chunk 40 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 0.0070 chunk 54 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 115 optimal weight: 0.0980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN D 521 GLN H 39 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.043585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.035659 restraints weight = 110152.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036710 restraints weight = 68727.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.037291 restraints weight = 49410.822| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13914 Z= 0.164 Angle : 0.648 12.299 18930 Z= 0.321 Chirality : 0.044 0.214 2166 Planarity : 0.004 0.049 2382 Dihedral : 7.598 84.925 2376 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.14 % Allowed : 0.42 % Favored : 99.44 % 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: -1.66 (0.21), residues: 1653 helix: 0.30 (0.34), residues: 213 sheet: -0.93 (0.24), residues: 471 loop : -1.53 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 86 HIS 0.003 0.001 HIS J 100D PHE 0.029 0.002 PHE G 67 TYR 0.020 0.001 TYR K 88 ARG 0.015 0.001 ARG J 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2744.16 seconds wall clock time: 51 minutes 4.63 seconds (3064.63 seconds total)