Starting phenix.real_space_refine on Fri Jul 3 11:24:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kej_22839/07_2026/7kej_22839.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kej_22839/07_2026/7kej_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_2026/7kej_22839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kej_22839/07_2026/7kej_22839.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7kej_22839/07_2026/7kej_22839.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kej_22839/07_2026/7kej_22839.cif" model { file = "/net/cci-nas-00/data/ceres_data/7kej_22839/07_2026/7kej_22839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kej_22839/07_2026/7kej_22839.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13806 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 984 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "K" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "C" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 984 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "A" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "G" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 984 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "J" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.93, per 1000 atoms: 0.21 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: 1.16 Conformation dependent library (CDL) restraints added in 745.0 milliseconds 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: 0.43 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: 2.48 Time building geometry restraints manager: 1.58 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 - 17.76: 7863 17.76 - 35.53: 174 35.53 - 53.29: 42 53.29 - 71.05: 21 71.05 - 88.82: 15 Dihedral angle restraints: 8115 sinusoidal: 3159 harmonic: 4956 Sorted by residual: dihedral pdb=" CB CYS B 108 " pdb=" SG CYS B 108 " pdb=" SG CYS B 135 " pdb=" CB CYS B 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.12 -37.12 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS C 108 " pdb=" SG CYS C 108 " pdb=" SG CYS C 135 " pdb=" CB CYS C 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.11 -37.11 1 1.00e+01 1.00e-02 1.94e+01 dihedral pdb=" CB CYS A 108 " pdb=" SG CYS A 108 " pdb=" SG CYS A 135 " pdb=" CB CYS A 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.11 -37.11 1 1.00e+01 1.00e-02 1.94e+01 ... (remaining 8112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1529 0.094 - 0.187: 507 0.187 - 0.281: 92 0.281 - 0.375: 34 0.375 - 0.468: 25 Chirality restraints: 2187 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.02e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 ... (remaining 2184 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 228 " -0.045 2.00e-02 2.50e+03 4.88e-02 2.98e+01 pdb=" CG ASN C 228 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN C 228 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 228 " 0.079 2.00e-02 2.50e+03 pdb=" C1 NAG C 403 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 228 " 0.045 2.00e-02 2.50e+03 4.86e-02 2.96e+01 pdb=" CG ASN B 228 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 228 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 228 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG B 403 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 228 " 0.045 2.00e-02 2.50e+03 4.86e-02 2.95e+01 pdb=" CG ASN A 228 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 228 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 228 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG A 403 " 0.058 2.00e-02 2.50e+03 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 3 1.94 - 2.68: 491 2.68 - 3.42: 17447 3.42 - 4.16: 34283 4.16 - 4.90: 57572 Nonbonded interactions: 109796 Sorted by model distance: nonbonded pdb=" OE1 GLU G 102 " pdb=" OH TYR G 112 " model vdw 1.201 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'A' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'G' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'D' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.690 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 : 10.031 88.816 4905 Min Nonbonded Distance : 1.201 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.001 ARG C 85 TYR 0.066 0.009 TYR B 99 PHE 0.020 0.005 PHE C 248 TRP 0.050 0.008 TRP A 86 HIS 0.006 0.002 HIS D 602 Details of bonding type rmsd/Z covalent geometry : bond 0.02057 / 1.07 (14115) covalent geometry : angle 1.72519 / 1.15 (19179) SS BOND : bond 0.00533 / 0.36 ( 18) SS BOND : angle 2.54134 / 1.63 ( 36) hydrogen bonds : bond 0.15777 / 10.74 ( 505) hydrogen bonds : angle 7.13199 / 4.98 ( 1290) link_ALPHA1-3 : bond 0.07638 / 3.83 ( 3) link_ALPHA1-3 : angle 4.60971 / 2.16 ( 9) link_ALPHA1-6 : bond 0.05251 / 2.63 ( 3) link_ALPHA1-6 : angle 3.86840 / 1.82 ( 9) link_BETA1-4 : bond 0.07226 / 4.28 ( 6) link_BETA1-4 : angle 5.11355 / 2.97 ( 18) link_NAG-ASN : bond 0.07784 / 5.34 ( 12) link_NAG-ASN : angle 2.50639 / 1.61 ( 36) *********************** 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 : 0.414 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: 0.6826 (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: 0.6177 (tm-30) REVERT: K 17 THR cc_start: 0.8371 (m) cc_final: 0.7924 (m) REVERT: K 30 TYR cc_start: 0.6838 (m-80) cc_final: 0.6620 (m-80) 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: 0.6601 (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: 0.6929 (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: 0.6215 (tm-30) REVERT: J 91 ASP cc_start: 0.8823 (t0) cc_final: 0.8594 (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: 0.1383 time to fit residues: 72.4881 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 : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3542 r_free = 0.3542 target = 0.103225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.081830 restraints weight = 29376.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.083975 restraints weight = 52087.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.084168 restraints weight = 32248.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.085581 restraints weight = 22953.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.085607 restraints weight = 20250.794| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14157 Z= 0.157 Angle : 0.653 9.628 19287 Z= 0.348 Chirality : 0.046 0.231 2187 Planarity : 0.005 0.072 2442 Dihedral : 4.876 18.661 1884 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.86 % Allowed : 7.66 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 1704 helix: 2.37 (0.38), residues: 159 sheet: 0.54 (0.19), residues: 645 loop : 0.55 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 596 TYR 0.022 0.002 TYR B 261 PHE 0.017 0.002 PHE F 592 TRP 0.016 0.001 TRP C 86 HIS 0.006 0.001 HIS L 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (14115) covalent geometry : angle 0.63657 / 0.34 (19179) SS BOND : bond 0.00243 / 0.16 ( 18) SS BOND : angle 1.05364 / 0.66 ( 36) hydrogen bonds : bond 0.04944 / 3.28 ( 505) hydrogen bonds : angle 5.80064 / 4.01 ( 1290) link_ALPHA1-3 : bond 0.00742 / 0.37 ( 3) link_ALPHA1-3 : angle 1.27333 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00495 / 0.25 ( 3) link_ALPHA1-6 : angle 1.58468 / 0.90 ( 9) link_BETA1-4 : bond 0.00727 / 0.44 ( 6) link_BETA1-4 : angle 3.11121 / 1.90 ( 18) link_NAG-ASN : bond 0.00799 / 0.55 ( 12) link_NAG-ASN : angle 2.41903 / 1.63 ( 36) *********************** 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 255 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: H 81 MET cc_start: 0.7412 (tmm) cc_final: 0.6795 (tmm) REVERT: H 82 GLU cc_start: 0.7981 (tp30) cc_final: 0.7382 (tp30) REVERT: K 97 LEU cc_start: 0.9134 (tp) cc_final: 0.8867 (tp) REVERT: E 527 ILE cc_start: 0.7986 (mm) cc_final: 0.7603 (pt) REVERT: E 611 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6461 (mm-30) REVERT: C 281 ILE cc_start: 0.7905 (pt) cc_final: 0.7695 (pt) REVERT: I 48 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.5899 (ttm) REVERT: I 82 GLU cc_start: 0.7927 (tp30) cc_final: 0.7671 (tp30) REVERT: I 111 TYR cc_start: 0.8592 (m-80) cc_final: 0.8304 (m-80) REVERT: L 51 ASN cc_start: 0.7691 (p0) cc_final: 0.7388 (p0) REVERT: L 57 ILE cc_start: 0.8373 (mm) cc_final: 0.8153 (tp) REVERT: L 74 ILE cc_start: 0.8790 (mt) cc_final: 0.8456 (mt) REVERT: F 527 ILE cc_start: 0.7964 (mm) cc_final: 0.7732 (pt) REVERT: F 577 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8556 (t) REVERT: G 81 MET cc_start: 0.8013 (tmm) cc_final: 0.7742 (tmm) REVERT: D 527 ILE cc_start: 0.7867 (mm) cc_final: 0.7615 (pt) REVERT: D 602 HIS cc_start: 0.6120 (OUTLIER) cc_final: 0.4988 (t-90) outliers start: 27 outliers final: 16 residues processed: 244 average time/residue: 0.1157 time to fit residues: 42.2366 Evaluate side-chains 196 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 267 SER 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 I residue 48 MET 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 18 VAL 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 95 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN H 65 GLN ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** L 16 GLN A 44 GLN G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN D 551 GLN D 595 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.097550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.075276 restraints weight = 29985.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.076478 restraints weight = 57199.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.077103 restraints weight = 45740.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.078231 restraints weight = 28761.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.078378 restraints weight = 25246.595| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 14157 Z= 0.306 Angle : 0.722 9.200 19287 Z= 0.380 Chirality : 0.048 0.208 2187 Planarity : 0.006 0.057 2442 Dihedral : 4.870 19.198 1884 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.48 % Allowed : 10.01 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 1704 helix: 1.61 (0.39), residues: 177 sheet: 0.24 (0.20), residues: 657 loop : 0.00 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 38 TYR 0.013 0.002 TYR A 220 PHE 0.024 0.003 PHE B 159 TRP 0.013 0.002 TRP B 104 HIS 0.009 0.002 HIS D 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00739 / 0.31 (14115) covalent geometry : angle 0.70458 / 0.38 (19179) SS BOND : bond 0.00431 / 0.24 ( 18) SS BOND : angle 2.21518 / 1.34 ( 36) hydrogen bonds : bond 0.05273 / 3.51 ( 505) hydrogen bonds : angle 5.62220 / 3.88 ( 1290) link_ALPHA1-3 : bond 0.00778 / 0.39 ( 3) link_ALPHA1-3 : angle 0.96731 / 0.53 ( 9) link_ALPHA1-6 : bond 0.00698 / 0.35 ( 3) link_ALPHA1-6 : angle 1.64805 / 0.93 ( 9) link_BETA1-4 : bond 0.00520 / 0.29 ( 6) link_BETA1-4 : angle 2.80231 / 1.76 ( 18) link_NAG-ASN : bond 0.00128 / 0.09 ( 12) link_NAG-ASN : angle 2.26881 / 1.45 ( 36) *********************** 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 238 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: H 81 MET cc_start: 0.7570 (tmm) cc_final: 0.6899 (tmm) REVERT: E 527 ILE cc_start: 0.8299 (mm) cc_final: 0.8079 (pt) REVERT: I 82 GLU cc_start: 0.8026 (tp30) cc_final: 0.7745 (tp30) REVERT: F 552 ASP cc_start: 0.7611 (t0) cc_final: 0.7269 (t0) REVERT: A 100 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6786 (mp0) outliers start: 36 outliers final: 23 residues processed: 220 average time/residue: 0.1109 time to fit residues: 37.1530 Evaluate side-chains 203 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 159 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 152 optimal weight: 0.1980 chunk 102 optimal weight: 0.0670 chunk 125 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 D 602 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.100076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.077774 restraints weight = 29530.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.078933 restraints weight = 52776.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.079679 restraints weight = 40726.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081239 restraints weight = 25796.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.081385 restraints weight = 21880.592| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14157 Z= 0.123 Angle : 0.583 10.873 19287 Z= 0.301 Chirality : 0.044 0.199 2187 Planarity : 0.004 0.032 2442 Dihedral : 4.517 18.333 1884 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 2.48 % Allowed : 10.21 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 1704 helix: 1.84 (0.40), residues: 177 sheet: 0.22 (0.19), residues: 657 loop : -0.05 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 40 TYR 0.012 0.001 TYR B 99 PHE 0.019 0.001 PHE H 64 TRP 0.008 0.001 TRP L 34 HIS 0.003 0.001 HIS D 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (14115) covalent geometry : angle 0.56799 / 0.30 (19179) SS BOND : bond 0.00364 / 0.26 ( 18) SS BOND : angle 1.86807 / 1.18 ( 36) hydrogen bonds : bond 0.03951 / 2.63 ( 505) hydrogen bonds : angle 5.38674 / 3.72 ( 1290) link_ALPHA1-3 : bond 0.00698 / 0.35 ( 3) link_ALPHA1-3 : angle 1.36110 / 0.75 ( 9) link_ALPHA1-6 : bond 0.00706 / 0.35 ( 3) link_ALPHA1-6 : angle 1.62778 / 0.91 ( 9) link_BETA1-4 : bond 0.00532 / 0.32 ( 6) link_BETA1-4 : angle 2.32840 / 1.44 ( 18) link_NAG-ASN : bond 0.00341 / 0.23 ( 12) link_NAG-ASN : angle 1.64651 / 1.10 ( 36) *********************** 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 240 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: H 48 MET cc_start: 0.7037 (mtm) cc_final: 0.6700 (ttm) REVERT: H 81 MET cc_start: 0.7553 (tmm) cc_final: 0.6789 (tmm) REVERT: H 111 TYR cc_start: 0.8731 (m-80) cc_final: 0.8460 (m-80) REVERT: K 35 TYR cc_start: 0.8903 (m-80) cc_final: 0.8614 (m-10) REVERT: E 552 ASP cc_start: 0.7215 (t0) cc_final: 0.7002 (t0) REVERT: C 100 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: F 552 ASP cc_start: 0.7561 (t0) cc_final: 0.7269 (t0) REVERT: A 100 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6454 (mp0) REVERT: D 552 ASP cc_start: 0.7172 (t0) cc_final: 0.6950 (t0) outliers start: 36 outliers final: 18 residues processed: 228 average time/residue: 0.1122 time to fit residues: 38.2958 Evaluate side-chains 202 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLU 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 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 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 602 HIS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 540 GLU 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 92 optimal weight: 7.9990 chunk 53 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 65 GLN ** 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 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 = 0.3478 r_free = 0.3478 target = 0.099266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.076638 restraints weight = 29707.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078061 restraints weight = 49778.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078701 restraints weight = 38027.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.079821 restraints weight = 24572.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.080004 restraints weight = 22327.367| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14157 Z= 0.151 Angle : 0.568 8.389 19287 Z= 0.296 Chirality : 0.044 0.264 2187 Planarity : 0.004 0.049 2442 Dihedral : 4.378 20.110 1884 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.48 % Allowed : 10.28 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 1704 helix: 1.90 (0.40), residues: 177 sheet: 0.19 (0.20), residues: 627 loop : -0.05 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 28 TYR 0.008 0.001 TYR C 99 PHE 0.013 0.002 PHE F 592 TRP 0.007 0.001 TRP C 104 HIS 0.009 0.001 HIS D 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (14115) covalent geometry : angle 0.55647 / 0.29 (19179) SS BOND : bond 0.00473 / 0.34 ( 18) SS BOND : angle 1.50247 / 0.96 ( 36) hydrogen bonds : bond 0.03953 / 2.64 ( 505) hydrogen bonds : angle 5.25606 / 3.63 ( 1290) link_ALPHA1-3 : bond 0.00640 / 0.32 ( 3) link_ALPHA1-3 : angle 1.16844 / 0.65 ( 9) link_ALPHA1-6 : bond 0.00536 / 0.27 ( 3) link_ALPHA1-6 : angle 1.52340 / 0.86 ( 9) link_BETA1-4 : bond 0.00441 / 0.26 ( 6) link_BETA1-4 : angle 2.23211 / 1.38 ( 18) link_NAG-ASN : bond 0.00189 / 0.13 ( 12) link_NAG-ASN : angle 1.54683 / 1.03 ( 36) *********************** 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 224 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.7127 (pttt) cc_final: 0.6882 (pttm) REVERT: B 100 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: H 48 MET cc_start: 0.7041 (mtm) cc_final: 0.6669 (ttm) REVERT: H 81 MET cc_start: 0.7612 (tmm) cc_final: 0.6881 (tmm) REVERT: E 552 ASP cc_start: 0.7302 (t0) cc_final: 0.7082 (t0) REVERT: C 100 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: A 100 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6342 (mp0) REVERT: D 552 ASP cc_start: 0.7198 (t0) cc_final: 0.6988 (t0) outliers start: 36 outliers final: 26 residues processed: 211 average time/residue: 0.1121 time to fit residues: 35.8973 Evaluate side-chains 205 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 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 25 ASP Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain C residue 269 THR 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 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 84 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 31 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 105 optimal weight: 0.0270 chunk 113 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN ** G 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 = 0.3504 r_free = 0.3504 target = 0.100711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.078302 restraints weight = 29305.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.079762 restraints weight = 49143.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.080290 restraints weight = 40274.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.081101 restraints weight = 25920.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.081337 restraints weight = 23359.917| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14157 Z= 0.101 Angle : 0.521 8.571 19287 Z= 0.271 Chirality : 0.043 0.181 2187 Planarity : 0.004 0.055 2442 Dihedral : 4.133 18.285 1884 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.14 % Allowed : 11.66 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1704 helix: 2.04 (0.40), residues: 177 sheet: 0.24 (0.19), residues: 654 loop : -0.06 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 19 TYR 0.008 0.001 TYR A 214 PHE 0.010 0.001 PHE A 290 TRP 0.007 0.001 TRP B 288 HIS 0.003 0.001 HIS L 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (14115) covalent geometry : angle 0.51135 / 0.27 (19179) SS BOND : bond 0.00196 / 0.14 ( 18) SS BOND : angle 1.21019 / 0.70 ( 36) hydrogen bonds : bond 0.03334 / 2.24 ( 505) hydrogen bonds : angle 5.08836 / 3.52 ( 1290) link_ALPHA1-3 : bond 0.00675 / 0.34 ( 3) link_ALPHA1-3 : angle 1.37679 / 0.76 ( 9) link_ALPHA1-6 : bond 0.00571 / 0.29 ( 3) link_ALPHA1-6 : angle 1.50991 / 0.85 ( 9) link_BETA1-4 : bond 0.00517 / 0.31 ( 6) link_BETA1-4 : angle 2.05102 / 1.27 ( 18) link_NAG-ASN : bond 0.00326 / 0.22 ( 12) link_NAG-ASN : angle 1.21201 / 0.84 ( 36) *********************** 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 241 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6560 (mp0) REVERT: H 48 MET cc_start: 0.6899 (mtm) cc_final: 0.6590 (ttm) REVERT: H 81 MET cc_start: 0.7509 (tmm) cc_final: 0.6710 (tmm) REVERT: H 82 GLU cc_start: 0.8100 (tp30) cc_final: 0.7824 (tp30) REVERT: H 111 TYR cc_start: 0.8736 (m-80) cc_final: 0.8512 (m-80) REVERT: K 38 LYS cc_start: 0.8228 (mmmt) cc_final: 0.7956 (mmtt) REVERT: C 100 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: I 82 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7717 (mm-30) REVERT: L 35 TYR cc_start: 0.8826 (m-80) cc_final: 0.8421 (m-80) REVERT: F 552 ASP cc_start: 0.7247 (t0) cc_final: 0.7033 (t0) REVERT: A 100 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6256 (mp0) outliers start: 31 outliers final: 20 residues processed: 229 average time/residue: 0.1118 time to fit residues: 38.8147 Evaluate side-chains 210 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 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 82 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 269 THR 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 602 HIS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain J residue 21 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 39 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 6 optimal weight: 0.0970 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 65 GLN ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.097939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.076408 restraints weight = 29500.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.076386 restraints weight = 52454.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076929 restraints weight = 46326.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.078787 restraints weight = 29752.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079059 restraints weight = 20700.596| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14157 Z= 0.208 Angle : 0.615 8.671 19287 Z= 0.320 Chirality : 0.045 0.187 2187 Planarity : 0.005 0.037 2442 Dihedral : 4.401 23.237 1884 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.20), residues: 1704 helix: 1.93 (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 ARG 0.008 0.001 ARG K 40 TYR 0.010 0.001 TYR K 85 PHE 0.017 0.002 PHE B 159 TRP 0.007 0.001 TRP B 104 HIS 0.003 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (14115) covalent geometry : angle 0.60492 / 0.32 (19179) SS BOND : bond 0.00437 / 0.27 ( 18) SS BOND : angle 1.41782 / 0.96 ( 36) hydrogen bonds : bond 0.04263 / 2.82 ( 505) hydrogen bonds : angle 5.06897 / 3.50 ( 1290) link_ALPHA1-3 : bond 0.00715 / 0.36 ( 3) link_ALPHA1-3 : angle 1.02071 / 0.58 ( 9) link_ALPHA1-6 : bond 0.00626 / 0.31 ( 3) link_ALPHA1-6 : angle 1.57417 / 0.89 ( 9) link_BETA1-4 : bond 0.00294 / 0.17 ( 6) link_BETA1-4 : angle 2.21294 / 1.38 ( 18) link_NAG-ASN : bond 0.00193 / 0.14 ( 12) link_NAG-ASN : angle 1.56282 / 1.02 ( 36) *********************** 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 218 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: H 81 MET cc_start: 0.7583 (tmm) cc_final: 0.6823 (tmm) REVERT: K 38 LYS cc_start: 0.8251 (mmmt) cc_final: 0.7955 (mmtt) REVERT: C 100 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: I 60 TYR cc_start: 0.7461 (m-80) cc_final: 0.7137 (m-80) REVERT: F 552 ASP cc_start: 0.7372 (t0) cc_final: 0.7150 (t0) REVERT: A 100 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6245 (mp0) outliers start: 32 outliers final: 24 residues processed: 206 average time/residue: 0.1053 time to fit residues: 33.4213 Evaluate side-chains 200 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 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 C residue 269 THR 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 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 57 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 84 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 16 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.098367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075873 restraints weight = 29257.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.076317 restraints weight = 48995.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.077053 restraints weight = 39381.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.078438 restraints weight = 28308.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078636 restraints weight = 25288.872| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14157 Z= 0.167 Angle : 0.579 7.169 19287 Z= 0.302 Chirality : 0.044 0.187 2187 Planarity : 0.004 0.034 2442 Dihedral : 4.314 22.860 1884 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.21 % Allowed : 12.56 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.20), residues: 1704 helix: 1.91 (0.39), residues: 177 sheet: -0.05 (0.19), residues: 654 loop : -0.22 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 40 TYR 0.008 0.001 TYR A 109 PHE 0.013 0.002 PHE F 592 TRP 0.008 0.001 TRP B 104 HIS 0.003 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (14115) covalent geometry : angle 0.56845 / 0.30 (19179) SS BOND : bond 0.00362 / 0.23 ( 18) SS BOND : angle 1.50561 / 1.01 ( 36) hydrogen bonds : bond 0.03847 / 2.55 ( 505) hydrogen bonds : angle 5.10603 / 3.54 ( 1290) link_ALPHA1-3 : bond 0.00657 / 0.33 ( 3) link_ALPHA1-3 : angle 1.14475 / 0.64 ( 9) link_ALPHA1-6 : bond 0.00558 / 0.28 ( 3) link_ALPHA1-6 : angle 1.54356 / 0.87 ( 9) link_BETA1-4 : bond 0.00356 / 0.22 ( 6) link_BETA1-4 : angle 2.09223 / 1.31 ( 18) link_NAG-ASN : bond 0.00167 / 0.12 ( 12) link_NAG-ASN : angle 1.33219 / 0.89 ( 36) *********************** 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 220 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6583 (mp0) REVERT: B 161 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8805 (mt) REVERT: K 38 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7745 (mmtt) REVERT: K 39 PRO cc_start: 0.8590 (Cg_exo) cc_final: 0.8217 (Cg_endo) REVERT: C 100 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6555 (mp0) REVERT: I 60 TYR cc_start: 0.7469 (m-80) cc_final: 0.7210 (m-80) REVERT: A 100 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: G 60 TYR cc_start: 0.7631 (m-80) cc_final: 0.7391 (m-80) outliers start: 32 outliers final: 22 residues processed: 211 average time/residue: 0.1057 time to fit residues: 34.4480 Evaluate side-chains 201 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 C residue 269 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain 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 21 THR Chi-restraints excluded: chain J residue 84 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 2 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 90 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN E 551 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.098815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076410 restraints weight = 29513.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.077652 restraints weight = 48944.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.078239 restraints weight = 40945.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.079479 restraints weight = 26338.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.079625 restraints weight = 22820.142| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14157 Z= 0.144 Angle : 0.586 9.535 19287 Z= 0.306 Chirality : 0.044 0.282 2187 Planarity : 0.004 0.036 2442 Dihedral : 4.266 22.279 1884 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.07 % Allowed : 13.11 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1704 helix: 1.97 (0.39), residues: 177 sheet: -0.02 (0.19), residues: 654 loop : -0.21 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 40 TYR 0.008 0.001 TYR A 109 PHE 0.014 0.001 PHE H 29 TRP 0.008 0.001 TRP B 104 HIS 0.003 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 (14115) covalent geometry : angle 0.57672 / 0.30 (19179) SS BOND : bond 0.00264 / 0.18 ( 18) SS BOND : angle 1.36651 / 0.90 ( 36) hydrogen bonds : bond 0.03672 / 2.44 ( 505) hydrogen bonds : angle 5.05652 / 3.52 ( 1290) link_ALPHA1-3 : bond 0.00717 / 0.36 ( 3) link_ALPHA1-3 : angle 1.16428 / 0.65 ( 9) link_ALPHA1-6 : bond 0.00590 / 0.30 ( 3) link_ALPHA1-6 : angle 1.54087 / 0.87 ( 9) link_BETA1-4 : bond 0.00402 / 0.24 ( 6) link_BETA1-4 : angle 2.06872 / 1.29 ( 18) link_NAG-ASN : bond 0.00188 / 0.14 ( 12) link_NAG-ASN : angle 1.24821 / 0.84 ( 36) *********************** 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 222 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: H 10 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8117 (mm-30) REVERT: H 48 MET cc_start: 0.7028 (mtm) cc_final: 0.6738 (ttm) REVERT: H 81 MET cc_start: 0.7261 (tmm) cc_final: 0.6767 (tmm) REVERT: H 82 GLU cc_start: 0.8182 (tp30) cc_final: 0.7662 (tp30) REVERT: C 100 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: A 100 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6281 (mp0) outliers start: 30 outliers final: 25 residues processed: 212 average time/residue: 0.0992 time to fit residues: 32.2709 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 : 0.538 ------------------------------------------------------------------------------- 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 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 C residue 269 THR Chi-restraints excluded: chain I residue 86 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 L residue 87 CYS Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 57 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 140 optimal weight: 0.0020 chunk 85 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** G 65 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN D 551 GLN D 602 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.098373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.076798 restraints weight = 29305.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.077542 restraints weight = 49424.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.078178 restraints weight = 36178.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.078932 restraints weight = 26411.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.079191 restraints weight = 25401.354| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4898 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= 0.176 Angle : 0.609 9.435 19287 Z= 0.318 Chirality : 0.044 0.263 2187 Planarity : 0.004 0.040 2442 Dihedral : 4.397 23.767 1884 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.21 % Allowed : 13.32 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1704 helix: 1.96 (0.39), residues: 177 sheet: -0.03 (0.19), residues: 654 loop : -0.26 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 40 TYR 0.012 0.001 TYR C 241 PHE 0.015 0.002 PHE H 29 TRP 0.007 0.001 TRP B 104 HIS 0.007 0.001 HIS J 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (14115) covalent geometry : angle 0.59840 / 0.32 (19179) SS BOND : bond 0.00342 / 0.22 ( 18) SS BOND : angle 1.75364 / 1.00 ( 36) hydrogen bonds : bond 0.03869 / 2.57 ( 505) hydrogen bonds : angle 5.05579 / 3.51 ( 1290) link_ALPHA1-3 : bond 0.00722 / 0.36 ( 3) link_ALPHA1-3 : angle 1.07582 / 0.61 ( 9) link_ALPHA1-6 : bond 0.00560 / 0.28 ( 3) link_ALPHA1-6 : angle 1.53751 / 0.87 ( 9) link_BETA1-4 : bond 0.00338 / 0.20 ( 6) link_BETA1-4 : angle 2.09283 / 1.31 ( 18) link_NAG-ASN : bond 0.00181 / 0.14 ( 12) link_NAG-ASN : angle 1.33391 / 0.89 ( 36) ********************** 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 212 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: B 161 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8738 (mt) REVERT: H 48 MET cc_start: 0.6859 (mtm) cc_final: 0.6641 (ttm) REVERT: H 81 MET cc_start: 0.7300 (tmm) cc_final: 0.6810 (tmm) REVERT: H 82 GLU cc_start: 0.8067 (tp30) cc_final: 0.7554 (tp30) REVERT: C 100 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: A 100 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6353 (mp0) outliers start: 32 outliers final: 25 residues processed: 202 average time/residue: 0.1022 time to fit residues: 31.3495 Evaluate side-chains 202 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 C residue 269 THR Chi-restraints excluded: chain I residue 86 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 L residue 87 CYS Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 0.0050 chunk 146 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 62 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 overall best weight: 0.9956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.099232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.076322 restraints weight = 29385.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.077591 restraints weight = 45275.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.078045 restraints weight = 38826.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.080051 restraints weight = 24984.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.080192 restraints weight = 17504.865| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14157 Z= 0.134 Angle : 0.588 9.202 19287 Z= 0.307 Chirality : 0.043 0.196 2187 Planarity : 0.004 0.035 2442 Dihedral : 4.279 22.604 1884 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.00 % Allowed : 13.53 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.20), residues: 1704 helix: 2.05 (0.40), residues: 177 sheet: -0.04 (0.19), residues: 660 loop : -0.19 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 19 TYR 0.011 0.001 TYR A 99 PHE 0.015 0.001 PHE H 29 TRP 0.008 0.001 TRP G 47 HIS 0.004 0.001 HIS J 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (14115) covalent geometry : angle 0.57694 / 0.30 (19179) SS BOND : bond 0.00327 / 0.20 ( 18) SS BOND : angle 1.87382 / 1.01 ( 36) hydrogen bonds : bond 0.03525 / 2.35 ( 505) hydrogen bonds : angle 5.02618 / 3.50 ( 1290) link_ALPHA1-3 : bond 0.00711 / 0.36 ( 3) link_ALPHA1-3 : angle 1.21437 / 0.68 ( 9) link_ALPHA1-6 : bond 0.00515 / 0.26 ( 3) link_ALPHA1-6 : angle 1.49920 / 0.85 ( 9) link_BETA1-4 : bond 0.00374 / 0.23 ( 6) link_BETA1-4 : angle 2.03176 / 1.27 ( 18) link_NAG-ASN : bond 0.00229 / 0.17 ( 12) link_NAG-ASN : angle 1.15453 / 0.78 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2081.81 seconds wall clock time: 37 minutes 0.22 seconds (2220.22 seconds total)