Starting phenix.real_space_refine on Thu Jul 31 22:29:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kej_22839/07_2025/7kej_22839.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kej_22839/07_2025/7kej_22839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kej_22839/07_2025/7kej_22839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kej_22839/07_2025/7kej_22839.map" model { file = "/net/cci-nas-00/data/ceres_data/7kej_22839/07_2025/7kej_22839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kej_22839/07_2025/7kej_22839.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 8718 2.51 5 N 2322 2.21 5 O 2709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13806 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 984 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "K" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "C" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 984 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "A" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "G" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 984 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "J" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.75, per 1000 atoms: 0.85 Number of scatterers: 13806 At special positions: 0 Unit cell: (156.56, 160.68, 124.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2709 8.00 N 2322 7.00 C 8718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.04 Simple disulfide: pdb=" SG CYS E 601 " - pdb=" SG CYS E 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 401 " - " ASN A 257 " " NAG A 402 " - " ASN A 268 " " NAG A 403 " - " ASN A 228 " " NAG B 401 " - " ASN B 257 " " NAG B 402 " - " ASN B 268 " " NAG B 403 " - " ASN B 228 " " NAG C 401 " - " ASN C 257 " " NAG C 402 " - " ASN C 268 " " NAG C 403 " - " ASN C 228 " " NAG M 1 " - " ASN E 563 " " NAG N 1 " - " ASN F 563 " " NAG O 1 " - " ASN D 563 " Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 1.7 seconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 30 sheets defined 15.7% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 25 through 28 Processing helix chain 'K' and resid 78 through 82 Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 553 through 575 removed outlier: 4.848A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 598 removed outlier: 3.845A pdb=" N ARG E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'L' and resid 25 through 28 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 553 through 575 removed outlier: 4.847A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.845A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'J' and resid 25 through 28 Processing helix chain 'J' and resid 78 through 82 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 553 through 575 removed outlier: 4.847A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.845A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 36 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 36 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 114 removed outlier: 6.405A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG B 136 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 14.122A pdb=" N THR B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ASP B 237 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 277 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN B 243 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE B 274 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASN H 101 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.070A pdb=" N CYS H 96 " --> pdb=" O TRP H 118 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TRP H 118 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG H 98 " --> pdb=" O ASP H 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU K 108 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL K 12 " --> pdb=" O LEU K 108 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP K 34 " --> pdb=" O VAL K 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU K 108 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL K 12 " --> pdb=" O LEU K 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AB1, first strand: chain 'E' and resid 601 through 602 removed outlier: 6.641A pdb=" N CYS E 601 " --> pdb=" O GLU F 611 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 610 through 611 Processing sheet with id=AB3, first strand: chain 'C' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB6, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.405A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 14.122A pdb=" N THR C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ASP C 237 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL C 277 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN C 243 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE C 274 " --> pdb=" O GLN I 99 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASN I 101 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.070A pdb=" N CYS I 96 " --> pdb=" O TRP I 118 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP I 118 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG I 98 " --> pdb=" O ASP I 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU L 108 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL L 12 " --> pdb=" O LEU L 108 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU L 108 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL L 12 " --> pdb=" O LEU L 108 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AC3, first strand: chain 'F' and resid 601 through 602 removed outlier: 6.641A pdb=" N CYS F 601 " --> pdb=" O GLU D 611 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.881A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AC7, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.405A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 14.122A pdb=" N THR A 217 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ASP A 237 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A 277 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN A 243 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE A 274 " --> pdb=" O GLN G 99 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN G 101 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 7.070A pdb=" N CYS G 96 " --> pdb=" O TRP G 118 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP G 118 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG G 98 " --> pdb=" O ASP G 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'J' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU J 108 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL J 12 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP J 34 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 9 through 13 removed outlier: 6.607A pdb=" N VAL J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU J 108 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL J 12 " --> pdb=" O LEU J 108 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 18 through 23 532 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.19 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2797 1.32 - 1.45: 4352 1.45 - 1.58: 6842 1.58 - 1.72: 55 1.72 - 1.85: 69 Bond restraints: 14115 Sorted by residual: bond pdb=" CB HIS C 154 " pdb=" CG HIS C 154 " ideal model delta sigma weight residual 1.497 1.404 0.093 1.40e-02 5.10e+03 4.41e+01 bond pdb=" CB HIS B 154 " pdb=" CG HIS B 154 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.35e+01 bond pdb=" CB HIS A 154 " pdb=" CG HIS A 154 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.33e+01 bond pdb=" CB TYR B 99 " pdb=" CG TYR B 99 " ideal model delta sigma weight residual 1.512 1.381 0.131 2.20e-02 2.07e+03 3.53e+01 bond pdb=" CB TYR C 99 " pdb=" CG TYR C 99 " ideal model delta sigma weight residual 1.512 1.381 0.131 2.20e-02 2.07e+03 3.52e+01 ... (remaining 14110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 16160 2.24 - 4.48: 2505 4.48 - 6.72: 450 6.72 - 8.97: 55 8.97 - 11.21: 9 Bond angle restraints: 19179 Sorted by residual: angle pdb=" N ARG K 60 " pdb=" CA ARG K 60 " pdb=" C ARG K 60 " ideal model delta sigma weight residual 114.56 103.35 11.21 1.27e+00 6.20e-01 7.79e+01 angle pdb=" N ARG J 60 " pdb=" CA ARG J 60 " pdb=" C ARG J 60 " ideal model delta sigma weight residual 114.56 103.37 11.19 1.27e+00 6.20e-01 7.76e+01 angle pdb=" N ARG L 60 " pdb=" CA ARG L 60 " pdb=" C ARG L 60 " ideal model delta sigma weight residual 114.56 103.37 11.19 1.27e+00 6.20e-01 7.76e+01 angle pdb=" C LEU B 122 " pdb=" N PRO B 123 " pdb=" CA PRO B 123 " ideal model delta sigma weight residual 119.85 127.15 -7.30 1.01e+00 9.80e-01 5.23e+01 angle pdb=" C LEU C 122 " pdb=" N PRO C 123 " pdb=" CA PRO C 123 " ideal model delta sigma weight residual 119.85 127.14 -7.29 1.01e+00 9.80e-01 5.21e+01 ... (remaining 19174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 8340 21.17 - 42.35: 171 42.35 - 63.52: 39 63.52 - 84.70: 30 84.70 - 105.87: 21 Dihedral angle restraints: 8601 sinusoidal: 3645 harmonic: 4956 Sorted by residual: dihedral pdb=" CB CYS B 108 " pdb=" SG CYS B 108 " pdb=" SG CYS B 135 " pdb=" CB CYS B 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.12 -37.12 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS C 108 " pdb=" SG CYS C 108 " pdb=" SG CYS C 135 " pdb=" CB CYS C 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.11 -37.11 1 1.00e+01 1.00e-02 1.94e+01 dihedral pdb=" CB CYS A 108 " pdb=" SG CYS A 108 " pdb=" SG CYS A 135 " pdb=" CB CYS A 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.11 -37.11 1 1.00e+01 1.00e-02 1.94e+01 ... (remaining 8598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1529 0.094 - 0.187: 507 0.187 - 0.281: 92 0.281 - 0.375: 34 0.375 - 0.468: 25 Chirality restraints: 2187 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.02e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 ... (remaining 2184 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 228 " -0.045 2.00e-02 2.50e+03 4.88e-02 2.98e+01 pdb=" CG ASN C 228 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN C 228 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 228 " 0.079 2.00e-02 2.50e+03 pdb=" C1 NAG C 403 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 228 " 0.045 2.00e-02 2.50e+03 4.86e-02 2.96e+01 pdb=" CG ASN B 228 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 228 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 228 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG B 403 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 228 " 0.045 2.00e-02 2.50e+03 4.86e-02 2.95e+01 pdb=" CG ASN A 228 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 228 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 228 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG A 403 " 0.058 2.00e-02 2.50e+03 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 3 1.94 - 2.68: 491 2.68 - 3.42: 17447 3.42 - 4.16: 34283 4.16 - 4.90: 57572 Nonbonded interactions: 109796 Sorted by model distance: nonbonded pdb=" OE1 GLU G 102 " pdb=" OH TYR G 112 " model vdw 1.201 3.040 nonbonded pdb=" OE1 GLU H 102 " pdb=" OH TYR H 112 " model vdw 1.201 3.040 nonbonded pdb=" OE1 GLU I 102 " pdb=" OH TYR I 112 " model vdw 1.202 3.040 nonbonded pdb=" CD GLU G 102 " pdb=" OH TYR G 112 " model vdw 2.293 3.270 nonbonded pdb=" CD GLU I 102 " pdb=" OH TYR I 112 " model vdw 2.293 3.270 ... (remaining 109791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 40.000 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.148 14157 Z= 1.076 Angle : 1.739 11.208 19287 Z= 1.152 Chirality : 0.107 0.468 2187 Planarity : 0.008 0.038 2442 Dihedral : 11.824 105.871 5391 Min Nonbonded Distance : 1.201 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1704 helix: 1.45 (0.35), residues: 156 sheet: 0.90 (0.20), residues: 594 loop : 0.77 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.008 TRP A 86 HIS 0.006 0.002 HIS D 602 PHE 0.020 0.005 PHE C 248 TYR 0.066 0.009 TYR B 99 ARG 0.006 0.001 ARG C 85 Details of bonding type rmsd link_NAG-ASN : bond 0.07784 ( 12) link_NAG-ASN : angle 2.50639 ( 36) link_ALPHA1-6 : bond 0.05251 ( 3) link_ALPHA1-6 : angle 3.86840 ( 9) link_BETA1-4 : bond 0.07226 ( 6) link_BETA1-4 : angle 5.11355 ( 18) link_ALPHA1-3 : bond 0.07638 ( 3) link_ALPHA1-3 : angle 4.60971 ( 9) hydrogen bonds : bond 0.15777 ( 505) hydrogen bonds : angle 7.13199 ( 1290) SS BOND : bond 0.00533 ( 18) SS BOND : angle 2.54134 ( 36) covalent geometry : bond 0.02057 (14115) covalent geometry : angle 1.72519 (19179) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 ARG cc_start: 0.7902 (tpt90) cc_final: 0.7629 (mpt-90) REVERT: H 13 LYS cc_start: 0.7170 (mttm) cc_final: 0.6827 (mppt) REVERT: H 115 MET cc_start: 0.8962 (mpp) cc_final: 0.8641 (mpp) REVERT: K 16 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6179 (tm-30) REVERT: K 17 THR cc_start: 0.8371 (m) cc_final: 0.7928 (m) REVERT: K 30 TYR cc_start: 0.6837 (m-80) cc_final: 0.6620 (m-80) REVERT: K 74 ILE cc_start: 0.8975 (mt) cc_final: 0.8748 (mt) REVERT: K 91 ASP cc_start: 0.8784 (t0) cc_final: 0.8580 (t0) REVERT: E 527 ILE cc_start: 0.7701 (mm) cc_final: 0.7351 (pt) REVERT: C 278 ASN cc_start: 0.8247 (t0) cc_final: 0.8039 (t0) REVERT: C 281 ILE cc_start: 0.7935 (pt) cc_final: 0.7572 (pt) REVERT: I 13 LYS cc_start: 0.7176 (mttm) cc_final: 0.6767 (mptt) REVERT: I 115 MET cc_start: 0.9000 (mpp) cc_final: 0.8683 (mpp) REVERT: L 16 GLN cc_start: 0.7097 (mm-40) cc_final: 0.6605 (tt0) REVERT: L 28 ARG cc_start: 0.7445 (mtt-85) cc_final: 0.7243 (ttm110) REVERT: L 51 ASN cc_start: 0.8398 (p0) cc_final: 0.8163 (p0) REVERT: L 91 ASP cc_start: 0.8757 (t0) cc_final: 0.8519 (t0) REVERT: F 527 ILE cc_start: 0.7826 (mm) cc_final: 0.7593 (pt) REVERT: F 588 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8900 (mmtp) REVERT: G 13 LYS cc_start: 0.7393 (mttm) cc_final: 0.6930 (mppt) REVERT: G 115 MET cc_start: 0.8951 (mpp) cc_final: 0.8661 (mpp) REVERT: J 16 GLN cc_start: 0.7201 (mm-40) cc_final: 0.6218 (tm-30) REVERT: J 91 ASP cc_start: 0.8823 (t0) cc_final: 0.8595 (t0) REVERT: D 527 ILE cc_start: 0.7508 (mm) cc_final: 0.7250 (pt) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.3750 time to fit residues: 196.0248 Evaluate side-chains 187 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.102723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.081766 restraints weight = 29202.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.081430 restraints weight = 48130.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.081941 restraints weight = 47388.599| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14157 Z= 0.173 Angle : 0.671 10.063 19287 Z= 0.355 Chirality : 0.047 0.237 2187 Planarity : 0.005 0.076 2442 Dihedral : 9.103 80.449 2370 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.79 % Allowed : 7.66 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.19), residues: 1704 helix: 2.31 (0.38), residues: 159 sheet: 0.54 (0.19), residues: 645 loop : 0.51 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 86 HIS 0.006 0.001 HIS J 96 PHE 0.019 0.002 PHE F 592 TYR 0.022 0.002 TYR B 261 ARG 0.006 0.001 ARG C 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 12) link_NAG-ASN : angle 2.40911 ( 36) link_ALPHA1-6 : bond 0.00583 ( 3) link_ALPHA1-6 : angle 1.47402 ( 9) link_BETA1-4 : bond 0.00727 ( 6) link_BETA1-4 : angle 3.44382 ( 18) link_ALPHA1-3 : bond 0.01065 ( 3) link_ALPHA1-3 : angle 1.73800 ( 9) hydrogen bonds : bond 0.04954 ( 505) hydrogen bonds : angle 5.81648 ( 1290) SS BOND : bond 0.00258 ( 18) SS BOND : angle 1.11218 ( 36) covalent geometry : bond 0.00395 (14115) covalent geometry : angle 0.65302 (19179) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 81 MET cc_start: 0.7485 (tmm) cc_final: 0.6855 (tmm) REVERT: H 82 GLU cc_start: 0.7983 (tp30) cc_final: 0.7425 (tp30) REVERT: K 16 GLN cc_start: 0.6197 (mm-40) cc_final: 0.5967 (tm-30) REVERT: K 17 THR cc_start: 0.7574 (m) cc_final: 0.7351 (m) REVERT: K 57 ILE cc_start: 0.8187 (mm) cc_final: 0.7958 (tp) REVERT: K 97 LEU cc_start: 0.9156 (tp) cc_final: 0.8883 (tp) REVERT: E 527 ILE cc_start: 0.7968 (mm) cc_final: 0.7578 (pt) REVERT: E 611 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6509 (mm-30) REVERT: C 281 ILE cc_start: 0.7866 (pt) cc_final: 0.7654 (pt) REVERT: I 82 GLU cc_start: 0.7949 (tp30) cc_final: 0.7707 (tp30) REVERT: I 111 TYR cc_start: 0.8595 (m-80) cc_final: 0.8324 (m-80) REVERT: L 51 ASN cc_start: 0.7647 (p0) cc_final: 0.7345 (p0) REVERT: F 527 ILE cc_start: 0.7937 (mm) cc_final: 0.7729 (pt) REVERT: F 577 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8520 (t) REVERT: G 81 MET cc_start: 0.8089 (tmm) cc_final: 0.7775 (tmm) REVERT: J 17 THR cc_start: 0.8017 (m) cc_final: 0.7389 (m) REVERT: D 527 ILE cc_start: 0.7793 (mm) cc_final: 0.7556 (pt) REVERT: D 602 HIS cc_start: 0.6167 (OUTLIER) cc_final: 0.5032 (t-90) outliers start: 26 outliers final: 15 residues processed: 242 average time/residue: 0.3046 time to fit residues: 109.2767 Evaluate side-chains 198 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 146 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 102 optimal weight: 0.2980 chunk 55 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 84 optimal weight: 0.0000 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN H 65 GLN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN E 551 GLN E 595 GLN C 44 GLN I 65 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 GLN G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN D 551 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.100909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.079957 restraints weight = 29427.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.079684 restraints weight = 49700.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.080214 restraints weight = 48898.554| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14157 Z= 0.160 Angle : 0.613 8.474 19287 Z= 0.322 Chirality : 0.045 0.204 2187 Planarity : 0.004 0.042 2442 Dihedral : 8.294 72.881 2370 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.07 % Allowed : 9.04 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1704 helix: 1.85 (0.39), residues: 177 sheet: 0.42 (0.20), residues: 615 loop : 0.21 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 86 HIS 0.020 0.002 HIS D 602 PHE 0.015 0.002 PHE F 592 TYR 0.016 0.001 TYR K 30 ARG 0.005 0.001 ARG J 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 12) link_NAG-ASN : angle 1.90369 ( 36) link_ALPHA1-6 : bond 0.00840 ( 3) link_ALPHA1-6 : angle 1.81225 ( 9) link_BETA1-4 : bond 0.00714 ( 6) link_BETA1-4 : angle 2.75440 ( 18) link_ALPHA1-3 : bond 0.01370 ( 3) link_ALPHA1-3 : angle 0.88636 ( 9) hydrogen bonds : bond 0.04374 ( 505) hydrogen bonds : angle 5.49362 ( 1290) SS BOND : bond 0.00369 ( 18) SS BOND : angle 1.85338 ( 36) covalent geometry : bond 0.00373 (14115) covalent geometry : angle 0.59652 (19179) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: H 81 MET cc_start: 0.7519 (tmm) cc_final: 0.6794 (tmm) REVERT: H 82 GLU cc_start: 0.8016 (tp30) cc_final: 0.7808 (tp30) REVERT: K 16 GLN cc_start: 0.6389 (mm-40) cc_final: 0.6085 (tm-30) REVERT: E 527 ILE cc_start: 0.8134 (mm) cc_final: 0.7795 (pt) REVERT: I 48 MET cc_start: 0.6671 (mtm) cc_final: 0.6144 (ttm) REVERT: I 82 GLU cc_start: 0.8015 (tp30) cc_final: 0.7789 (tp30) REVERT: I 83 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6511 (tt) REVERT: L 51 ASN cc_start: 0.7490 (p0) cc_final: 0.7227 (p0) REVERT: F 552 ASP cc_start: 0.7383 (t0) cc_final: 0.7058 (t0) REVERT: A 100 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6790 (mp0) outliers start: 30 outliers final: 20 residues processed: 217 average time/residue: 0.2510 time to fit residues: 81.0655 Evaluate side-chains 196 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain I residue 65 GLN Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 79 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 0.0000 chunk 51 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** D 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN D 602 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.097607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.075401 restraints weight = 29545.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.076226 restraints weight = 58005.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.077055 restraints weight = 47199.266| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 14157 Z= 0.263 Angle : 0.681 10.794 19287 Z= 0.351 Chirality : 0.048 0.232 2187 Planarity : 0.005 0.049 2442 Dihedral : 7.746 62.448 2370 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.24 % Allowed : 9.04 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.19), residues: 1704 helix: 1.65 (0.39), residues: 177 sheet: 0.13 (0.20), residues: 630 loop : -0.05 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS D 602 PHE 0.026 0.003 PHE H 64 TYR 0.012 0.002 TYR A 220 ARG 0.005 0.001 ARG L 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 12) link_NAG-ASN : angle 1.99274 ( 36) link_ALPHA1-6 : bond 0.00977 ( 3) link_ALPHA1-6 : angle 2.06397 ( 9) link_BETA1-4 : bond 0.00471 ( 6) link_BETA1-4 : angle 2.56803 ( 18) link_ALPHA1-3 : bond 0.01267 ( 3) link_ALPHA1-3 : angle 0.93048 ( 9) hydrogen bonds : bond 0.04849 ( 505) hydrogen bonds : angle 5.43417 ( 1290) SS BOND : bond 0.00403 ( 18) SS BOND : angle 2.14752 ( 36) covalent geometry : bond 0.00639 (14115) covalent geometry : angle 0.66434 (19179) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: B 161 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8837 (mt) REVERT: H 81 MET cc_start: 0.7657 (tmm) cc_final: 0.7024 (tmm) REVERT: K 6 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.6399 (mt0) REVERT: K 35 TYR cc_start: 0.8892 (m-80) cc_final: 0.8584 (m-10) REVERT: C 100 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: C 161 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8790 (mt) REVERT: I 48 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6209 (ttm) REVERT: I 82 GLU cc_start: 0.8035 (tp30) cc_final: 0.7821 (tp30) REVERT: F 552 ASP cc_start: 0.7596 (t0) cc_final: 0.7275 (t0) REVERT: A 100 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6571 (mp0) outliers start: 47 outliers final: 29 residues processed: 227 average time/residue: 0.3201 time to fit residues: 107.6899 Evaluate side-chains 210 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 138 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 160 optimal weight: 0.4980 chunk 95 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN E 514 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.098850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.077908 restraints weight = 29527.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.077647 restraints weight = 52755.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.078273 restraints weight = 46334.588| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14157 Z= 0.172 Angle : 0.595 8.818 19287 Z= 0.308 Chirality : 0.046 0.229 2187 Planarity : 0.004 0.034 2442 Dihedral : 7.219 56.129 2370 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.55 % Allowed : 10.35 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1704 helix: 1.78 (0.39), residues: 177 sheet: 0.07 (0.19), residues: 654 loop : -0.13 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 34 HIS 0.005 0.001 HIS D 602 PHE 0.013 0.002 PHE F 592 TYR 0.010 0.001 TYR A 109 ARG 0.006 0.001 ARG K 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 12) link_NAG-ASN : angle 1.60975 ( 36) link_ALPHA1-6 : bond 0.00999 ( 3) link_ALPHA1-6 : angle 2.04956 ( 9) link_BETA1-4 : bond 0.00475 ( 6) link_BETA1-4 : angle 2.29137 ( 18) link_ALPHA1-3 : bond 0.01340 ( 3) link_ALPHA1-3 : angle 0.78504 ( 9) hydrogen bonds : bond 0.04142 ( 505) hydrogen bonds : angle 5.32376 ( 1290) SS BOND : bond 0.00324 ( 18) SS BOND : angle 1.19076 ( 36) covalent geometry : bond 0.00409 (14115) covalent geometry : angle 0.58435 (19179) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.7133 (pttt) cc_final: 0.6891 (pttm) REVERT: B 100 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: B 161 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8860 (mt) REVERT: C 100 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: C 161 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8744 (mt) REVERT: I 48 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6448 (ttm) REVERT: F 552 ASP cc_start: 0.7670 (t0) cc_final: 0.7416 (t0) REVERT: A 100 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6421 (mp0) outliers start: 37 outliers final: 22 residues processed: 215 average time/residue: 0.3007 time to fit residues: 95.2964 Evaluate side-chains 203 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 84 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.077092 restraints weight = 29392.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.077419 restraints weight = 49380.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.078180 restraints weight = 39797.659| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14157 Z= 0.164 Angle : 0.587 9.057 19287 Z= 0.303 Chirality : 0.045 0.219 2187 Planarity : 0.004 0.045 2442 Dihedral : 6.753 47.057 2370 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.97 % Allowed : 11.39 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1704 helix: 1.88 (0.39), residues: 177 sheet: -0.02 (0.19), residues: 654 loop : -0.18 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.003 0.001 HIS A 154 PHE 0.013 0.002 PHE F 592 TYR 0.009 0.001 TYR A 109 ARG 0.008 0.001 ARG J 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 12) link_NAG-ASN : angle 1.41784 ( 36) link_ALPHA1-6 : bond 0.00857 ( 3) link_ALPHA1-6 : angle 1.81523 ( 9) link_BETA1-4 : bond 0.00503 ( 6) link_BETA1-4 : angle 2.20580 ( 18) link_ALPHA1-3 : bond 0.01317 ( 3) link_ALPHA1-3 : angle 0.71842 ( 9) hydrogen bonds : bond 0.03968 ( 505) hydrogen bonds : angle 5.22155 ( 1290) SS BOND : bond 0.00350 ( 18) SS BOND : angle 1.91450 ( 36) covalent geometry : bond 0.00392 (14115) covalent geometry : angle 0.57400 (19179) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: B 161 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8843 (mt) REVERT: H 48 MET cc_start: 0.6905 (mtm) cc_final: 0.6640 (ttm) REVERT: H 81 MET cc_start: 0.7442 (tmm) cc_final: 0.6933 (tmm) REVERT: C 100 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6656 (mp0) REVERT: C 161 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8759 (mt) REVERT: F 552 ASP cc_start: 0.7614 (t0) cc_final: 0.7414 (t0) REVERT: A 100 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6427 (mp0) outliers start: 43 outliers final: 27 residues processed: 218 average time/residue: 0.2901 time to fit residues: 95.7470 Evaluate side-chains 204 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 601 CYS Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 84 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 76 optimal weight: 0.0980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 GLN F 551 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.099874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.078542 restraints weight = 29412.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078324 restraints weight = 51278.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.079177 restraints weight = 49883.809| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14157 Z= 0.123 Angle : 0.565 8.834 19287 Z= 0.292 Chirality : 0.044 0.179 2187 Planarity : 0.004 0.032 2442 Dihedral : 6.299 59.894 2370 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.35 % Allowed : 12.28 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1704 helix: 1.99 (0.39), residues: 177 sheet: -0.01 (0.19), residues: 654 loop : -0.17 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 34 HIS 0.002 0.001 HIS L 96 PHE 0.011 0.001 PHE G 29 TYR 0.010 0.001 TYR A 214 ARG 0.011 0.001 ARG L 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 12) link_NAG-ASN : angle 1.21742 ( 36) link_ALPHA1-6 : bond 0.00689 ( 3) link_ALPHA1-6 : angle 1.54887 ( 9) link_BETA1-4 : bond 0.00557 ( 6) link_BETA1-4 : angle 2.16094 ( 18) link_ALPHA1-3 : bond 0.01327 ( 3) link_ALPHA1-3 : angle 0.85393 ( 9) hydrogen bonds : bond 0.03564 ( 505) hydrogen bonds : angle 5.10980 ( 1290) SS BOND : bond 0.00280 ( 18) SS BOND : angle 1.47974 ( 36) covalent geometry : bond 0.00287 (14115) covalent geometry : angle 0.55541 (19179) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: H 48 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6731 (ttm) REVERT: H 81 MET cc_start: 0.7442 (tmm) cc_final: 0.6894 (tmm) REVERT: H 82 GLU cc_start: 0.8150 (tp30) cc_final: 0.7717 (tp30) REVERT: K 17 THR cc_start: 0.7848 (m) cc_final: 0.7514 (t) REVERT: C 100 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: A 100 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6371 (mp0) outliers start: 34 outliers final: 24 residues processed: 203 average time/residue: 0.2432 time to fit residues: 74.6188 Evaluate side-chains 205 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 601 CYS Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 601 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 106 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.098548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.077932 restraints weight = 29490.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.079008 restraints weight = 63010.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.079858 restraints weight = 42135.502| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14157 Z= 0.183 Angle : 0.593 8.646 19287 Z= 0.309 Chirality : 0.044 0.178 2187 Planarity : 0.004 0.033 2442 Dihedral : 5.402 38.852 2370 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.69 % Allowed : 12.15 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.20), residues: 1704 helix: 1.95 (0.39), residues: 177 sheet: -0.10 (0.19), residues: 654 loop : -0.22 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.003 0.001 HIS C 154 PHE 0.017 0.002 PHE H 29 TYR 0.009 0.001 TYR B 214 ARG 0.007 0.001 ARG L 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 12) link_NAG-ASN : angle 1.36149 ( 36) link_ALPHA1-6 : bond 0.00265 ( 3) link_ALPHA1-6 : angle 1.91473 ( 9) link_BETA1-4 : bond 0.00491 ( 6) link_BETA1-4 : angle 2.27707 ( 18) link_ALPHA1-3 : bond 0.01237 ( 3) link_ALPHA1-3 : angle 0.79329 ( 9) hydrogen bonds : bond 0.04020 ( 505) hydrogen bonds : angle 5.08719 ( 1290) SS BOND : bond 0.00490 ( 18) SS BOND : angle 1.66200 ( 36) covalent geometry : bond 0.00441 (14115) covalent geometry : angle 0.58194 (19179) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: B 161 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8864 (mt) REVERT: B 278 ASN cc_start: 0.7936 (t0) cc_final: 0.7712 (t0) REVERT: H 81 MET cc_start: 0.7506 (tmm) cc_final: 0.7008 (tmm) REVERT: H 82 GLU cc_start: 0.8084 (tp30) cc_final: 0.7655 (tp30) REVERT: K 17 THR cc_start: 0.7794 (m) cc_final: 0.7456 (t) REVERT: C 100 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: I 60 TYR cc_start: 0.7581 (m-80) cc_final: 0.7374 (m-80) REVERT: A 100 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6421 (mp0) outliers start: 39 outliers final: 28 residues processed: 215 average time/residue: 0.2395 time to fit residues: 77.1213 Evaluate side-chains 215 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 601 CYS Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 601 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 111 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 71 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.100804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.079254 restraints weight = 28966.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.079519 restraints weight = 47460.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.080288 restraints weight = 38185.331| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14157 Z= 0.121 Angle : 0.572 9.034 19287 Z= 0.299 Chirality : 0.044 0.307 2187 Planarity : 0.004 0.032 2442 Dihedral : 5.052 37.796 2370 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.21 % Allowed : 12.49 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1704 helix: 1.54 (0.38), residues: 195 sheet: -0.03 (0.19), residues: 654 loop : -0.21 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 47 HIS 0.003 0.001 HIS L 96 PHE 0.011 0.001 PHE H 29 TYR 0.017 0.001 TYR C 99 ARG 0.015 0.000 ARG K 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 12) link_NAG-ASN : angle 1.13324 ( 36) link_ALPHA1-6 : bond 0.00210 ( 3) link_ALPHA1-6 : angle 1.71021 ( 9) link_BETA1-4 : bond 0.00511 ( 6) link_BETA1-4 : angle 2.15270 ( 18) link_ALPHA1-3 : bond 0.01204 ( 3) link_ALPHA1-3 : angle 1.23787 ( 9) hydrogen bonds : bond 0.03491 ( 505) hydrogen bonds : angle 5.06674 ( 1290) SS BOND : bond 0.00307 ( 18) SS BOND : angle 1.44428 ( 36) covalent geometry : bond 0.00282 (14115) covalent geometry : angle 0.56197 (19179) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: B 161 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8858 (mt) REVERT: B 278 ASN cc_start: 0.7946 (t0) cc_final: 0.7716 (t0) REVERT: B 288 TRP cc_start: 0.7007 (m100) cc_final: 0.6644 (m-10) REVERT: H 10 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8118 (mm-30) REVERT: H 82 GLU cc_start: 0.7981 (tp30) cc_final: 0.7757 (tp30) REVERT: K 17 THR cc_start: 0.7811 (m) cc_final: 0.7524 (t) REVERT: K 40 ARG cc_start: 0.7888 (ttm110) cc_final: 0.7660 (ttp-110) REVERT: C 100 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6477 (mp0) REVERT: A 100 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6262 (mp0) outliers start: 32 outliers final: 25 residues processed: 217 average time/residue: 0.2589 time to fit residues: 83.1139 Evaluate side-chains 213 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 601 CYS Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 601 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 131 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN E 551 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.099373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.078379 restraints weight = 29178.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.079595 restraints weight = 52787.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.080247 restraints weight = 39958.090| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14157 Z= 0.184 Angle : 0.618 9.576 19287 Z= 0.322 Chirality : 0.045 0.303 2187 Planarity : 0.005 0.049 2442 Dihedral : 5.234 37.610 2370 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.21 % Allowed : 12.49 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1704 helix: 1.58 (0.38), residues: 195 sheet: -0.07 (0.19), residues: 654 loop : -0.28 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.003 0.001 HIS A 154 PHE 0.014 0.002 PHE G 29 TYR 0.016 0.001 TYR C 99 ARG 0.014 0.001 ARG K 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 12) link_NAG-ASN : angle 1.36591 ( 36) link_ALPHA1-6 : bond 0.00070 ( 3) link_ALPHA1-6 : angle 1.81448 ( 9) link_BETA1-4 : bond 0.00415 ( 6) link_BETA1-4 : angle 2.29194 ( 18) link_ALPHA1-3 : bond 0.01132 ( 3) link_ALPHA1-3 : angle 0.94019 ( 9) hydrogen bonds : bond 0.04019 ( 505) hydrogen bonds : angle 5.04039 ( 1290) SS BOND : bond 0.00403 ( 18) SS BOND : angle 1.55796 ( 36) covalent geometry : bond 0.00446 (14115) covalent geometry : angle 0.60762 (19179) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: B 161 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8891 (mt) REVERT: B 278 ASN cc_start: 0.7968 (t0) cc_final: 0.7721 (t0) REVERT: B 288 TRP cc_start: 0.6904 (m100) cc_final: 0.6545 (m-10) REVERT: H 82 GLU cc_start: 0.7992 (tp30) cc_final: 0.7730 (tp30) REVERT: K 17 THR cc_start: 0.7841 (m) cc_final: 0.7541 (t) REVERT: C 100 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6455 (mp0) REVERT: A 100 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6348 (mp0) outliers start: 32 outliers final: 25 residues processed: 215 average time/residue: 0.2353 time to fit residues: 76.5267 Evaluate side-chains 216 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 601 CYS Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 601 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 83 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 49 optimal weight: 0.0770 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN ** D 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.100860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.080806 restraints weight = 29255.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.081142 restraints weight = 51849.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.081857 restraints weight = 42626.272| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14157 Z= 0.123 Angle : 0.592 10.168 19287 Z= 0.308 Chirality : 0.043 0.202 2187 Planarity : 0.004 0.032 2442 Dihedral : 5.017 36.991 2370 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.14 % Allowed : 12.91 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1704 helix: 1.63 (0.38), residues: 195 sheet: -0.01 (0.20), residues: 654 loop : -0.21 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS L 96 PHE 0.014 0.001 PHE H 29 TYR 0.017 0.001 TYR C 99 ARG 0.009 0.000 ARG L 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 12) link_NAG-ASN : angle 1.12304 ( 36) link_ALPHA1-6 : bond 0.00206 ( 3) link_ALPHA1-6 : angle 1.66412 ( 9) link_BETA1-4 : bond 0.00465 ( 6) link_BETA1-4 : angle 2.17504 ( 18) link_ALPHA1-3 : bond 0.01096 ( 3) link_ALPHA1-3 : angle 1.32836 ( 9) hydrogen bonds : bond 0.03466 ( 505) hydrogen bonds : angle 5.01075 ( 1290) SS BOND : bond 0.00340 ( 18) SS BOND : angle 1.75157 ( 36) covalent geometry : bond 0.00288 (14115) covalent geometry : angle 0.58137 (19179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4395.46 seconds wall clock time: 80 minutes 22.27 seconds (4822.27 seconds total)