Starting phenix.real_space_refine on Wed Mar 4 13:18:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kej_22839/03_2026/7kej_22839.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kej_22839/03_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_22839/03_2026/7kej_22839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kej_22839/03_2026/7kej_22839.map" model { file = "/net/cci-nas-00/data/ceres_data/7kej_22839/03_2026/7kej_22839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kej_22839/03_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-5986/lib/python3.9/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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.98, per 1000 atoms: 0.22 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: 1.15 Conformation dependent library (CDL) restraints added in 504.1 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: 0.38 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: 2.03 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2797 1.32 - 1.45: 4352 1.45 - 1.58: 6842 1.58 - 1.72: 55 1.72 - 1.85: 69 Bond restraints: 14115 Sorted by residual: bond pdb=" CB HIS C 154 " pdb=" CG HIS C 154 " ideal model delta sigma weight residual 1.497 1.404 0.093 1.40e-02 5.10e+03 4.41e+01 bond pdb=" CB HIS B 154 " pdb=" CG HIS B 154 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.35e+01 bond pdb=" CB HIS A 154 " pdb=" CG HIS A 154 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.33e+01 bond pdb=" CB TYR B 99 " pdb=" CG TYR B 99 " ideal model delta sigma weight residual 1.512 1.381 0.131 2.20e-02 2.07e+03 3.53e+01 bond pdb=" CB TYR C 99 " pdb=" CG TYR C 99 " ideal model delta sigma weight residual 1.512 1.381 0.131 2.20e-02 2.07e+03 3.52e+01 ... (remaining 14110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 16160 2.24 - 4.48: 2505 4.48 - 6.72: 450 6.72 - 8.97: 55 8.97 - 11.21: 9 Bond angle restraints: 19179 Sorted by residual: angle pdb=" N ARG K 60 " pdb=" CA ARG K 60 " pdb=" C ARG K 60 " ideal model delta sigma weight residual 114.56 103.35 11.21 1.27e+00 6.20e-01 7.79e+01 angle pdb=" N ARG J 60 " pdb=" CA ARG J 60 " pdb=" C ARG J 60 " ideal model delta sigma weight residual 114.56 103.37 11.19 1.27e+00 6.20e-01 7.76e+01 angle pdb=" N ARG L 60 " pdb=" CA ARG L 60 " pdb=" C ARG L 60 " ideal model delta sigma weight residual 114.56 103.37 11.19 1.27e+00 6.20e-01 7.76e+01 angle pdb=" C LEU B 122 " pdb=" N PRO B 123 " pdb=" CA PRO B 123 " ideal model delta sigma weight residual 119.85 127.15 -7.30 1.01e+00 9.80e-01 5.23e+01 angle pdb=" C LEU C 122 " pdb=" N PRO C 123 " pdb=" CA PRO C 123 " ideal model delta sigma weight residual 119.85 127.14 -7.29 1.01e+00 9.80e-01 5.21e+01 ... (remaining 19174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 8340 21.17 - 42.35: 171 42.35 - 63.52: 39 63.52 - 84.70: 30 84.70 - 105.87: 21 Dihedral angle restraints: 8601 sinusoidal: 3645 harmonic: 4956 Sorted by residual: dihedral pdb=" CB CYS B 108 " pdb=" SG CYS B 108 " pdb=" SG CYS B 135 " pdb=" CB CYS B 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.12 -37.12 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS C 108 " pdb=" SG CYS C 108 " pdb=" SG CYS C 135 " pdb=" CB CYS C 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.11 -37.11 1 1.00e+01 1.00e-02 1.94e+01 dihedral pdb=" CB CYS A 108 " pdb=" SG CYS A 108 " pdb=" SG CYS A 135 " pdb=" CB CYS A 135 " ideal model delta sinusoidal sigma weight residual 93.00 130.11 -37.11 1 1.00e+01 1.00e-02 1.94e+01 ... (remaining 8598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1529 0.094 - 0.187: 507 0.187 - 0.281: 92 0.281 - 0.375: 34 0.375 - 0.468: 25 Chirality restraints: 2187 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.02e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 ... (remaining 2184 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 228 " -0.045 2.00e-02 2.50e+03 4.88e-02 2.98e+01 pdb=" CG ASN C 228 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN C 228 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 228 " 0.079 2.00e-02 2.50e+03 pdb=" C1 NAG C 403 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 228 " 0.045 2.00e-02 2.50e+03 4.86e-02 2.96e+01 pdb=" CG ASN B 228 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 228 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 228 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG B 403 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 228 " 0.045 2.00e-02 2.50e+03 4.86e-02 2.95e+01 pdb=" CG ASN A 228 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 228 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 228 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG A 403 " 0.058 2.00e-02 2.50e+03 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 3 1.94 - 2.68: 491 2.68 - 3.42: 17447 3.42 - 4.16: 34283 4.16 - 4.90: 57572 Nonbonded interactions: 109796 Sorted by model distance: nonbonded pdb=" OE1 GLU G 102 " pdb=" OH TYR G 112 " model vdw 1.201 3.040 nonbonded pdb=" OE1 GLU H 102 " pdb=" OH TYR H 112 " model vdw 1.201 3.040 nonbonded pdb=" OE1 GLU I 102 " pdb=" OH TYR I 112 " model vdw 1.202 3.040 nonbonded pdb=" CD GLU G 102 " pdb=" OH TYR G 112 " model vdw 2.293 3.270 nonbonded pdb=" CD GLU I 102 " pdb=" OH TYR I 112 " model vdw 2.293 3.270 ... (remaining 109791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 1.360 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.300 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.148 14157 Z= 1.076 Angle : 1.739 11.208 19287 Z= 1.152 Chirality : 0.107 0.468 2187 Planarity : 0.008 0.038 2442 Dihedral : 11.824 105.871 5391 Min Nonbonded Distance : 1.201 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.02057 (14115) covalent geometry : angle 1.72519 (19179) SS BOND : bond 0.00533 ( 18) SS BOND : angle 2.54134 ( 36) hydrogen bonds : bond 0.15777 ( 505) hydrogen bonds : angle 7.13199 ( 1290) link_ALPHA1-3 : bond 0.07638 ( 3) link_ALPHA1-3 : angle 4.60971 ( 9) link_ALPHA1-6 : bond 0.05251 ( 3) link_ALPHA1-6 : angle 3.86840 ( 9) link_BETA1-4 : bond 0.07226 ( 6) link_BETA1-4 : angle 5.11355 ( 18) link_NAG-ASN : bond 0.07784 ( 12) link_NAG-ASN : angle 2.50639 ( 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 : 0.500 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: 0.1350 time to fit residues: 70.3451 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 : 0.523 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.103211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.082252 restraints weight = 29357.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.081829 restraints weight = 49445.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.082593 restraints weight = 48626.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.083749 restraints weight = 28269.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.084130 restraints weight = 23482.055| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14157 Z= 0.156 Angle : 0.660 9.640 19287 Z= 0.350 Chirality : 0.047 0.241 2187 Planarity : 0.005 0.071 2442 Dihedral : 9.094 80.643 2370 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.86 % Allowed : 7.80 % Favored : 90.34 % 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: 2.39 (0.37), residues: 159 sheet: 0.55 (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 0.016 0.002 PHE F 592 TRP 0.015 0.001 TRP C 86 HIS 0.006 0.001 HIS L 96 Details of bonding type rmsd covalent geometry : bond 0.00348 (14115) covalent geometry : angle 0.64241 (19179) SS BOND : bond 0.00325 ( 18) SS BOND : angle 1.05601 ( 36) hydrogen bonds : bond 0.04929 ( 505) hydrogen bonds : angle 5.78581 ( 1290) link_ALPHA1-3 : bond 0.01178 ( 3) link_ALPHA1-3 : angle 1.60564 ( 9) link_ALPHA1-6 : bond 0.00781 ( 3) link_ALPHA1-6 : angle 1.46292 ( 9) link_BETA1-4 : bond 0.00697 ( 6) link_BETA1-4 : angle 3.39991 ( 18) link_NAG-ASN : bond 0.00754 ( 12) link_NAG-ASN : angle 2.38779 ( 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 254 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: H 81 MET cc_start: 0.7460 (tmm) cc_final: 0.6815 (tmm) REVERT: H 82 GLU cc_start: 0.7998 (tp30) cc_final: 0.7430 (tp30) REVERT: K 97 LEU cc_start: 0.9148 (tp) cc_final: 0.8866 (tp) REVERT: E 527 ILE cc_start: 0.7985 (mm) cc_final: 0.7597 (pt) REVERT: E 611 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6470 (mm-30) REVERT: C 281 ILE cc_start: 0.7871 (pt) cc_final: 0.7665 (pt) REVERT: I 48 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.5890 (ttm) REVERT: I 111 TYR cc_start: 0.8588 (m-80) cc_final: 0.8299 (m-80) REVERT: L 51 ASN cc_start: 0.7719 (p0) cc_final: 0.7401 (p0) REVERT: F 527 ILE cc_start: 0.7941 (mm) cc_final: 0.7696 (pt) REVERT: F 577 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8557 (t) REVERT: G 81 MET cc_start: 0.8048 (tmm) cc_final: 0.7737 (tmm) REVERT: D 527 ILE cc_start: 0.7879 (mm) cc_final: 0.7616 (pt) REVERT: D 602 HIS cc_start: 0.6129 (OUTLIER) cc_final: 0.4992 (t-90) outliers start: 27 outliers final: 16 residues processed: 242 average time/residue: 0.1057 time to fit residues: 38.3528 Evaluate side-chains 195 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 0.0870 chunk 41 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN H 65 GLN ** H 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 = 0.3445 r_free = 0.3445 target = 0.097292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.074909 restraints weight = 29952.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076179 restraints weight = 56167.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.076729 restraints weight = 42380.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.079044 restraints weight = 27155.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.079064 restraints weight = 18498.975| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 14157 Z= 0.307 Angle : 0.734 9.504 19287 Z= 0.385 Chirality : 0.049 0.204 2187 Planarity : 0.006 0.060 2442 Dihedral : 8.461 70.320 2370 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.48 % Allowed : 9.39 % Favored : 88.13 % 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: 1.56 (0.39), residues: 177 sheet: 0.23 (0.20), residues: 657 loop : -0.02 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 38 TYR 0.014 0.002 TYR I 80 PHE 0.025 0.003 PHE B 159 TRP 0.013 0.002 TRP B 104 HIS 0.019 0.002 HIS D 602 Details of bonding type rmsd covalent geometry : bond 0.00739 (14115) covalent geometry : angle 0.71672 (19179) SS BOND : bond 0.00537 ( 18) SS BOND : angle 2.12814 ( 36) hydrogen bonds : bond 0.05374 ( 505) hydrogen bonds : angle 5.64203 ( 1290) link_ALPHA1-3 : bond 0.01262 ( 3) link_ALPHA1-3 : angle 0.72700 ( 9) link_ALPHA1-6 : bond 0.00937 ( 3) link_ALPHA1-6 : angle 1.95462 ( 9) link_BETA1-4 : bond 0.00490 ( 6) link_BETA1-4 : angle 2.85947 ( 18) link_NAG-ASN : bond 0.00124 ( 12) link_NAG-ASN : angle 2.22361 ( 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 241 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: E 527 ILE cc_start: 0.8336 (mm) cc_final: 0.8121 (pt) REVERT: F 552 ASP cc_start: 0.7667 (t0) cc_final: 0.7348 (t0) REVERT: A 100 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: J 80 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7280 (tm-30) outliers start: 36 outliers final: 23 residues processed: 224 average time/residue: 0.1005 time to fit residues: 34.0627 Evaluate side-chains 202 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 57 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 84 ASP 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: 0.9990 chunk 152 optimal weight: 0.0050 chunk 102 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 136 optimal weight: 0.0470 chunk 33 optimal weight: 0.0270 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 overall best weight: 0.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN D 551 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.100535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.078739 restraints weight = 29420.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.079190 restraints weight = 51270.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.079903 restraints weight = 45157.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081131 restraints weight = 28283.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.081301 restraints weight = 24330.310| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14157 Z= 0.110 Angle : 0.588 10.190 19287 Z= 0.302 Chirality : 0.044 0.213 2187 Planarity : 0.004 0.029 2442 Dihedral : 7.589 63.479 2370 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.62 % Allowed : 9.80 % Favored : 87.58 % 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: 1.83 (0.39), residues: 177 sheet: 0.25 (0.19), residues: 654 loop : -0.04 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 28 TYR 0.012 0.001 TYR B 99 PHE 0.022 0.001 PHE H 64 TRP 0.008 0.001 TRP G 47 HIS 0.003 0.001 HIS L 96 Details of bonding type rmsd covalent geometry : bond 0.00237 (14115) covalent geometry : angle 0.57321 (19179) SS BOND : bond 0.00235 ( 18) SS BOND : angle 1.86596 ( 36) hydrogen bonds : bond 0.03845 ( 505) hydrogen bonds : angle 5.41823 ( 1290) link_ALPHA1-3 : bond 0.01244 ( 3) link_ALPHA1-3 : angle 0.97540 ( 9) link_ALPHA1-6 : bond 0.00984 ( 3) link_ALPHA1-6 : angle 2.03654 ( 9) link_BETA1-4 : bond 0.00534 ( 6) link_BETA1-4 : angle 2.39754 ( 18) link_NAG-ASN : bond 0.00424 ( 12) link_NAG-ASN : angle 1.53753 ( 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 241 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6640 (mp0) REVERT: H 48 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6410 (ttm) REVERT: H 111 TYR cc_start: 0.8711 (m-80) cc_final: 0.8444 (m-80) REVERT: K 35 TYR cc_start: 0.8882 (m-80) cc_final: 0.8565 (m-10) REVERT: E 527 ILE cc_start: 0.8347 (mm) cc_final: 0.8141 (pt) REVERT: E 552 ASP cc_start: 0.7189 (t0) cc_final: 0.6975 (t0) REVERT: C 100 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: F 552 ASP cc_start: 0.7475 (t0) cc_final: 0.7217 (t0) REVERT: A 100 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6410 (mp0) outliers start: 38 outliers final: 19 residues processed: 229 average time/residue: 0.1116 time to fit residues: 37.9390 Evaluate side-chains 207 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 48 MET 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 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 A residue 267 SER Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 0.0370 chunk 53 optimal weight: 0.2980 chunk 149 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 114 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 GLN ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3500 r_free = 0.3500 target = 0.100651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.077985 restraints weight = 29623.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078684 restraints weight = 49106.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.079225 restraints weight = 43360.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.081102 restraints weight = 27655.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.081185 restraints weight = 20239.093| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14157 Z= 0.111 Angle : 0.550 8.183 19287 Z= 0.284 Chirality : 0.045 0.229 2187 Planarity : 0.004 0.041 2442 Dihedral : 6.870 54.917 2370 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.07 % Allowed : 10.56 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.41 (0.19), residues: 1704 helix: 2.02 (0.40), residues: 177 sheet: 0.27 (0.20), residues: 627 loop : 0.02 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 19 TYR 0.008 0.001 TYR B 261 PHE 0.013 0.001 PHE K 61 TRP 0.007 0.001 TRP L 34 HIS 0.003 0.001 HIS L 96 Details of bonding type rmsd covalent geometry : bond 0.00250 (14115) covalent geometry : angle 0.54056 (19179) SS BOND : bond 0.00230 ( 18) SS BOND : angle 1.06481 ( 36) hydrogen bonds : bond 0.03586 ( 505) hydrogen bonds : angle 5.20463 ( 1290) link_ALPHA1-3 : bond 0.01307 ( 3) link_ALPHA1-3 : angle 0.86845 ( 9) link_ALPHA1-6 : bond 0.00980 ( 3) link_ALPHA1-6 : angle 1.89623 ( 9) link_BETA1-4 : bond 0.00559 ( 6) link_BETA1-4 : angle 2.26697 ( 18) link_NAG-ASN : bond 0.00314 ( 12) link_NAG-ASN : angle 1.35467 ( 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 233 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: H 111 TYR cc_start: 0.8758 (m-80) cc_final: 0.8517 (m-80) REVERT: K 4 LEU cc_start: 0.7712 (mp) cc_final: 0.7407 (mt) REVERT: E 552 ASP cc_start: 0.7287 (t0) cc_final: 0.7037 (t0) REVERT: C 100 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: F 552 ASP cc_start: 0.7601 (t0) cc_final: 0.7355 (t0) REVERT: A 100 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6336 (mp0) REVERT: J 4 LEU cc_start: 0.7574 (mp) cc_final: 0.7353 (mt) outliers start: 30 outliers final: 21 residues processed: 223 average time/residue: 0.1075 time to fit residues: 35.9176 Evaluate side-chains 205 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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 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 A residue 267 SER Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 31 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 0.0170 chunk 9 optimal weight: 0.0170 chunk 115 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.099939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.079873 restraints weight = 29354.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.081604 restraints weight = 55471.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.081791 restraints weight = 35720.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.082122 restraints weight = 24927.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.082419 restraints weight = 22802.926| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14157 Z= 0.125 Angle : 0.553 8.470 19287 Z= 0.286 Chirality : 0.044 0.207 2187 Planarity : 0.004 0.036 2442 Dihedral : 6.473 51.665 2370 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.21 % Allowed : 11.18 % Favored : 86.61 % 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: 0.37 (0.20), residues: 1704 helix: 2.07 (0.40), residues: 177 sheet: 0.24 (0.20), residues: 627 loop : -0.02 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 19 TYR 0.010 0.001 TYR A 214 PHE 0.012 0.001 PHE A 290 TRP 0.006 0.001 TRP H 47 HIS 0.002 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00292 (14115) covalent geometry : angle 0.54340 (19179) SS BOND : bond 0.00209 ( 18) SS BOND : angle 1.14076 ( 36) hydrogen bonds : bond 0.03550 ( 505) hydrogen bonds : angle 5.06744 ( 1290) link_ALPHA1-3 : bond 0.01341 ( 3) link_ALPHA1-3 : angle 0.84133 ( 9) link_ALPHA1-6 : bond 0.00825 ( 3) link_ALPHA1-6 : angle 1.72300 ( 9) link_BETA1-4 : bond 0.00561 ( 6) link_BETA1-4 : angle 2.20109 ( 18) link_NAG-ASN : bond 0.00217 ( 12) link_NAG-ASN : angle 1.30537 ( 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 228 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: H 82 GLU cc_start: 0.8036 (tp30) cc_final: 0.7727 (tp30) REVERT: K 4 LEU cc_start: 0.7781 (mp) cc_final: 0.7379 (mt) REVERT: E 552 ASP cc_start: 0.7183 (t0) cc_final: 0.6942 (t0) REVERT: C 100 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6600 (mp0) REVERT: A 100 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6291 (mp0) outliers start: 32 outliers final: 20 residues processed: 215 average time/residue: 0.1016 time to fit residues: 32.9510 Evaluate side-chains 205 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 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 J residue 84 ASP Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 39 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 6 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 GLN ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.100647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.080083 restraints weight = 29240.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.082173 restraints weight = 52693.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.082337 restraints weight = 31321.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.082629 restraints weight = 23488.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.083013 restraints weight = 21213.467| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14157 Z= 0.107 Angle : 0.544 9.181 19287 Z= 0.279 Chirality : 0.043 0.171 2187 Planarity : 0.004 0.052 2442 Dihedral : 5.384 48.776 2370 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.28 % Allowed : 11.32 % Favored : 86.40 % 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: 0.41 (0.20), residues: 1704 helix: 2.07 (0.40), residues: 177 sheet: 0.33 (0.20), residues: 639 loop : -0.06 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 40 TYR 0.007 0.001 TYR H 94 PHE 0.008 0.001 PHE E 592 TRP 0.007 0.001 TRP C 288 HIS 0.002 0.001 HIS L 96 Details of bonding type rmsd covalent geometry : bond 0.00244 (14115) covalent geometry : angle 0.53532 (19179) SS BOND : bond 0.00166 ( 18) SS BOND : angle 1.12084 ( 36) hydrogen bonds : bond 0.03251 ( 505) hydrogen bonds : angle 4.94717 ( 1290) link_ALPHA1-3 : bond 0.01353 ( 3) link_ALPHA1-3 : angle 0.94606 ( 9) link_ALPHA1-6 : bond 0.00575 ( 3) link_ALPHA1-6 : angle 1.54042 ( 9) link_BETA1-4 : bond 0.00651 ( 6) link_BETA1-4 : angle 2.15406 ( 18) link_NAG-ASN : bond 0.00288 ( 12) link_NAG-ASN : angle 1.13520 ( 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 237 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: H 81 MET cc_start: 0.7482 (tmm) cc_final: 0.7070 (tmm) REVERT: H 82 GLU cc_start: 0.7940 (tp30) cc_final: 0.7549 (tp30) REVERT: H 111 TYR cc_start: 0.8738 (m-80) cc_final: 0.8510 (m-80) REVERT: C 100 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: I 60 TYR cc_start: 0.7319 (m-80) cc_final: 0.6997 (m-80) REVERT: L 35 TYR cc_start: 0.8872 (m-80) cc_final: 0.8542 (m-80) REVERT: A 100 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6323 (mp0) REVERT: A 113 ILE cc_start: 0.9064 (mm) cc_final: 0.8852 (mt) REVERT: G 103 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7968 (ptp) outliers start: 33 outliers final: 22 residues processed: 223 average time/residue: 0.0977 time to fit residues: 33.5841 Evaluate side-chains 212 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 117 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 540 GLU Chi-restraints excluded: chain E residue 602 HIS Chi-restraints excluded: chain C residue 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 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 21 THR Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 602 HIS 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: 5.9990 chunk 13 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.075473 restraints weight = 29649.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.077276 restraints weight = 56879.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.077416 restraints weight = 39201.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.077721 restraints weight = 26238.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.078140 restraints weight = 23136.341| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 14157 Z= 0.308 Angle : 0.703 9.116 19287 Z= 0.367 Chirality : 0.049 0.433 2187 Planarity : 0.006 0.047 2442 Dihedral : 5.767 38.736 2370 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.48 % Allowed : 11.87 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.19), residues: 1704 helix: 1.69 (0.39), residues: 177 sheet: -0.09 (0.19), residues: 654 loop : -0.32 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 580 TYR 0.014 0.002 TYR A 214 PHE 0.027 0.003 PHE C 159 TRP 0.009 0.001 TRP C 104 HIS 0.004 0.001 HIS D 549 Details of bonding type rmsd covalent geometry : bond 0.00748 (14115) covalent geometry : angle 0.69074 (19179) SS BOND : bond 0.00529 ( 18) SS BOND : angle 1.78433 ( 36) hydrogen bonds : bond 0.05049 ( 505) hydrogen bonds : angle 5.25391 ( 1290) link_ALPHA1-3 : bond 0.01167 ( 3) link_ALPHA1-3 : angle 0.71778 ( 9) link_ALPHA1-6 : bond 0.00106 ( 3) link_ALPHA1-6 : angle 2.08105 ( 9) link_BETA1-4 : bond 0.00383 ( 6) link_BETA1-4 : angle 2.45618 ( 18) link_NAG-ASN : bond 0.00366 ( 12) link_NAG-ASN : angle 1.83798 ( 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 221 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6724 (mp0) REVERT: H 81 MET cc_start: 0.7529 (tmm) cc_final: 0.7094 (tmm) REVERT: C 100 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: I 60 TYR cc_start: 0.7493 (m-80) cc_final: 0.7190 (m-80) REVERT: A 100 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: A 278 ASN cc_start: 0.7828 (t0) cc_final: 0.7434 (t0) outliers start: 36 outliers final: 24 residues processed: 207 average time/residue: 0.0981 time to fit residues: 31.4673 Evaluate side-chains 203 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 73 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 84 ASP 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 21 THR Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 2 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 131 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.076040 restraints weight = 29508.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076388 restraints weight = 48521.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.077084 restraints weight = 45187.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.078882 restraints weight = 28527.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.078988 restraints weight = 21897.110| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14157 Z= 0.130 Angle : 0.594 8.996 19287 Z= 0.311 Chirality : 0.045 0.347 2187 Planarity : 0.004 0.035 2442 Dihedral : 5.324 37.658 2370 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.86 % Allowed : 12.63 % Favored : 85.51 % 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: 0.10 (0.19), residues: 1704 helix: 1.95 (0.40), residues: 177 sheet: 0.19 (0.20), residues: 624 loop : -0.33 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 40 TYR 0.012 0.001 TYR C 241 PHE 0.011 0.001 PHE H 29 TRP 0.007 0.001 TRP B 104 HIS 0.004 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00300 (14115) covalent geometry : angle 0.58268 (19179) SS BOND : bond 0.00313 ( 18) SS BOND : angle 1.80609 ( 36) hydrogen bonds : bond 0.03791 ( 505) hydrogen bonds : angle 5.11132 ( 1290) link_ALPHA1-3 : bond 0.01234 ( 3) link_ALPHA1-3 : angle 1.23531 ( 9) link_ALPHA1-6 : bond 0.00143 ( 3) link_ALPHA1-6 : angle 1.70577 ( 9) link_BETA1-4 : bond 0.00464 ( 6) link_BETA1-4 : angle 2.16237 ( 18) link_NAG-ASN : bond 0.00252 ( 12) link_NAG-ASN : angle 1.24790 ( 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 210 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6385 (mp0) REVERT: H 10 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8125 (mm-30) REVERT: H 81 MET cc_start: 0.7616 (tmm) cc_final: 0.6955 (tmm) REVERT: H 82 GLU cc_start: 0.8156 (tp30) cc_final: 0.7759 (tp30) REVERT: C 100 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: I 60 TYR cc_start: 0.7449 (m-80) cc_final: 0.7118 (m-80) REVERT: I 115 MET cc_start: 0.8470 (mpp) cc_final: 0.8036 (mpp) REVERT: A 100 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6311 (mp0) REVERT: A 278 ASN cc_start: 0.7762 (t0) cc_final: 0.7368 (t0) REVERT: D 551 GLN cc_start: 0.7385 (mm110) cc_final: 0.7161 (mm-40) outliers start: 27 outliers final: 20 residues processed: 202 average time/residue: 0.1034 time to fit residues: 32.3535 Evaluate side-chains 198 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 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 269 THR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain F residue 602 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain 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 Chi-restraints excluded: chain D residue 602 HIS 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: 0.8980 chunk 60 optimal weight: 0.0050 chunk 142 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN K 41 GLN E 551 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.099129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.079565 restraints weight = 29207.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.081672 restraints weight = 52126.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.081752 restraints weight = 29362.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.082111 restraints weight = 22804.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.082326 restraints weight = 21277.287| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14157 Z= 0.176 Angle : 0.614 8.040 19287 Z= 0.324 Chirality : 0.045 0.283 2187 Planarity : 0.004 0.036 2442 Dihedral : 5.329 37.264 2370 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.66 % Allowed : 12.97 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.00 (0.40), residues: 177 sheet: -0.09 (0.19), residues: 660 loop : -0.27 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 19 TYR 0.009 0.001 TYR C 241 PHE 0.014 0.002 PHE B 159 TRP 0.008 0.001 TRP B 104 HIS 0.003 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00426 (14115) covalent geometry : angle 0.60079 (19179) SS BOND : bond 0.00310 ( 18) SS BOND : angle 2.01047 ( 36) hydrogen bonds : bond 0.03973 ( 505) hydrogen bonds : angle 5.06252 ( 1290) link_ALPHA1-3 : bond 0.01090 ( 3) link_ALPHA1-3 : angle 0.98545 ( 9) link_ALPHA1-6 : bond 0.00148 ( 3) link_ALPHA1-6 : angle 1.81282 ( 9) link_BETA1-4 : bond 0.00419 ( 6) link_BETA1-4 : angle 2.27707 ( 18) link_NAG-ASN : bond 0.00146 ( 12) link_NAG-ASN : angle 1.32600 ( 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 210 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6412 (mp0) REVERT: H 81 MET cc_start: 0.7540 (tmm) cc_final: 0.7024 (tmm) REVERT: H 82 GLU cc_start: 0.7936 (tp30) cc_final: 0.7511 (tp30) REVERT: K 4 LEU cc_start: 0.7895 (mp) cc_final: 0.7585 (mt) REVERT: K 80 GLU cc_start: 0.6766 (tm-30) cc_final: 0.6471 (tm-30) REVERT: C 100 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: A 100 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6299 (mp0) REVERT: A 278 ASN cc_start: 0.7879 (t0) cc_final: 0.7464 (t0) REVERT: J 40 ARG cc_start: 0.7798 (ptp90) cc_final: 0.7500 (ptp90) outliers start: 24 outliers final: 21 residues processed: 204 average time/residue: 0.0988 time to fit residues: 31.2795 Evaluate side-chains 206 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 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 269 THR Chi-restraints excluded: chain L residue 18 VAL 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 J residue 21 THR Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain D residue 602 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 109 optimal weight: 0.4980 chunk 99 optimal weight: 6.9990 chunk 8 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 62 optimal weight: 0.0070 chunk 82 optimal weight: 2.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** 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 = 0.3509 r_free = 0.3509 target = 0.100935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.079059 restraints weight = 29146.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079145 restraints weight = 47342.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.080043 restraints weight = 37675.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.081417 restraints weight = 27465.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.081671 restraints weight = 24998.219| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4989 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= 0.111 Angle : 0.577 9.075 19287 Z= 0.303 Chirality : 0.043 0.209 2187 Planarity : 0.004 0.033 2442 Dihedral : 4.916 36.259 2370 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.59 % Allowed : 13.04 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.16 (0.19), residues: 1704 helix: 1.66 (0.38), residues: 195 sheet: 0.31 (0.20), residues: 612 loop : -0.33 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 596 TYR 0.012 0.001 TYR A 99 PHE 0.009 0.001 PHE H 29 TRP 0.008 0.001 TRP A 288 HIS 0.003 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00251 (14115) covalent geometry : angle 0.56555 (19179) SS BOND : bond 0.00283 ( 18) SS BOND : angle 1.87135 ( 36) hydrogen bonds : bond 0.03282 ( 505) hydrogen bonds : angle 4.96483 ( 1290) link_ALPHA1-3 : bond 0.01080 ( 3) link_ALPHA1-3 : angle 1.42085 ( 9) link_ALPHA1-6 : bond 0.00261 ( 3) link_ALPHA1-6 : angle 1.60101 ( 9) link_BETA1-4 : bond 0.00486 ( 6) link_BETA1-4 : angle 2.16967 ( 18) link_NAG-ASN : bond 0.00322 ( 12) link_NAG-ASN : angle 1.05059 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1956.42 seconds wall clock time: 34 minutes 45.82 seconds (2085.82 seconds total)