Starting phenix.real_space_refine on Fri Jul 3 10:20:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kfb_22848/07_2026/7kfb_22848.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kfb_22848/07_2026/7kfb_22848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kfb_22848/07_2026/7kfb_22848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kfb_22848/07_2026/7kfb_22848.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7kfb_22848/07_2026/7kfb_22848.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kfb_22848/07_2026/7kfb_22848.cif" model { file = "/net/cci-nas-00/data/ceres_data/7kfb_22848/07_2026/7kfb_22848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kfb_22848/07_2026/7kfb_22848.cif" } resolution = 3.9 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 8505 2.51 5 N 2241 2.21 5 O 2670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13458 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1028 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "J" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "D" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 722 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, C, E, F, H, I, K, L, P, S, Q, T, R, U Time building chain proxies: 2.25, per 1000 atoms: 0.17 Number of scatterers: 13458 At special positions: 0 Unit cell: (116.39, 117.42, 119.48, 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 42 16.00 O 2670 8.00 N 2241 7.00 C 8505 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.04 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 101 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.02 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.05 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 101 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 101 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.02 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.05 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.05 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 O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 5 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 401 " - " ASN A 268 " " NAG A 402 " - " ASN A 238 " " NAG B 401 " - " ASN B 268 " " NAG B 402 " - " ASN B 238 " " NAG C 401 " - " ASN C 268 " " NAG C 402 " - " ASN C 238 " " NAG M 1 " - " ASN A 257 " " NAG N 1 " - " ASN A 228 " " NAG O 1 " - " ASN D 563 " " NAG P 1 " - " ASN B 257 " " NAG Q 1 " - " ASN B 228 " " NAG R 1 " - " ASN E 563 " " NAG S 1 " - " ASN C 257 " " NAG T 1 " - " ASN C 228 " " NAG U 1 " - " ASN F 563 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 442.8 milliseconds 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2982 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 30 sheets defined 16.6% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... 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 263 Processing helix chain 'G' and resid 67 through 70 Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 80 through 84 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 4.808A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 removed outlier: 3.590A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) 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 263 Processing helix chain 'H' and resid 67 through 70 Processing helix chain 'H' and resid 92 through 96 Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 80 through 84 Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 550 through 552 No H-bonds generated for 'chain 'E' and resid 550 through 552' Processing helix chain 'E' and resid 553 through 576 removed outlier: 4.809A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 removed outlier: 3.590A 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 263 Processing helix chain 'I' and resid 67 through 70 Processing helix chain 'I' and resid 92 through 96 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 4.809A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 removed outlier: 3.590A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 45 removed outlier: 6.712A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 114 through 119 removed outlier: 6.901A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL A 277 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLN A 243 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N ALA A 105 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 13.773A pdb=" N VAL A 180 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ASN A 107 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU A 178 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.707A pdb=" N THR G 83 " --> pdb=" O ASP G 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.005A pdb=" N MET G 37 " --> pdb=" O ARG G 53 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG G 53 " --> pdb=" O MET G 37 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP G 39 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.911A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.911A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 49 through 50 Processing sheet with id=AB2, first strand: chain 'B' and resid 43 through 45 removed outlier: 6.712A pdb=" N GLY B 36 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 114 through 119 removed outlier: 6.899A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL B 277 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLN B 243 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N ALA B 105 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 13.773A pdb=" N VAL B 180 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ASN B 107 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU B 178 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.707A pdb=" N THR H 83 " --> pdb=" O ASP H 78 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.005A pdb=" N MET H 37 " --> pdb=" O ARG H 53 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG H 53 " --> pdb=" O MET H 37 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP H 39 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB8, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU K 11 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU K 11 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 49 through 50 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 45 removed outlier: 6.713A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 114 through 119 removed outlier: 6.900A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 277 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N GLN C 243 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N ALA C 105 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 13.774A pdb=" N VAL C 180 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N ASN C 107 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU C 178 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AC6, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.708A pdb=" N THR I 83 " --> pdb=" O ASP I 78 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.005A pdb=" N MET I 37 " --> pdb=" O ARG I 53 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG I 53 " --> pdb=" O MET I 37 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP I 39 " --> pdb=" O ILE I 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 49 through 50 516 hydrogen bonds defined for protein. 1251 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: 1.79 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2537 1.32 - 1.46: 4800 1.46 - 1.60: 6340 1.60 - 1.74: 48 1.74 - 1.87: 39 Bond restraints: 13764 Sorted by residual: bond pdb=" CB TYR C 99 " pdb=" CG TYR C 99 " ideal model delta sigma weight residual 1.512 1.331 0.181 2.20e-02 2.07e+03 6.77e+01 bond pdb=" CB TYR A 99 " pdb=" CG TYR A 99 " ideal model delta sigma weight residual 1.512 1.331 0.181 2.20e-02 2.07e+03 6.77e+01 bond pdb=" CB TYR B 99 " pdb=" CG TYR B 99 " ideal model delta sigma weight residual 1.512 1.331 0.181 2.20e-02 2.07e+03 6.74e+01 bond pdb=" CB ILE L 107 " pdb=" CG1 ILE L 107 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" CB ILE K 107 " pdb=" CG1 ILE K 107 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 13759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 15397 2.26 - 4.53: 2687 4.53 - 6.79: 495 6.79 - 9.05: 84 9.05 - 11.31: 15 Bond angle restraints: 18678 Sorted by residual: angle pdb=" CA ASP H 78 " pdb=" CB ASP H 78 " pdb=" CG ASP H 78 " ideal model delta sigma weight residual 112.60 120.73 -8.13 1.00e+00 1.00e+00 6.61e+01 angle pdb=" CA ASP I 78 " pdb=" CB ASP I 78 " pdb=" CG ASP I 78 " ideal model delta sigma weight residual 112.60 120.70 -8.10 1.00e+00 1.00e+00 6.56e+01 angle pdb=" CA ASP G 78 " pdb=" CB ASP G 78 " pdb=" CG ASP G 78 " ideal model delta sigma weight residual 112.60 120.70 -8.10 1.00e+00 1.00e+00 6.56e+01 angle pdb=" N LEU A 186 " pdb=" CA LEU A 186 " pdb=" C LEU A 186 " ideal model delta sigma weight residual 113.16 124.47 -11.31 1.42e+00 4.96e-01 6.35e+01 angle pdb=" N LEU B 186 " pdb=" CA LEU B 186 " pdb=" C LEU B 186 " ideal model delta sigma weight residual 113.16 124.44 -11.28 1.42e+00 4.96e-01 6.31e+01 ... (remaining 18673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 7500 15.87 - 31.74: 186 31.74 - 47.61: 54 47.61 - 63.49: 33 63.49 - 79.36: 9 Dihedral angle restraints: 7782 sinusoidal: 3072 harmonic: 4710 Sorted by residual: dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 101 " pdb=" CB CYS I 101 " ideal model delta sinusoidal sigma weight residual 93.00 32.54 60.46 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 101 " pdb=" CB CYS G 101 " ideal model delta sinusoidal sigma weight residual 93.00 32.60 60.40 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 101 " pdb=" CB CYS H 101 " ideal model delta sinusoidal sigma weight residual 93.00 32.61 60.39 1 1.00e+01 1.00e-02 4.86e+01 ... (remaining 7779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1462 0.105 - 0.210: 510 0.210 - 0.315: 130 0.315 - 0.420: 47 0.420 - 0.525: 17 Chirality restraints: 2166 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.71e+01 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 9.65e+01 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.62e+01 ... (remaining 2163 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 99 " -0.105 2.00e-02 2.50e+03 5.64e-02 6.36e+01 pdb=" CG TYR B 99 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 99 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR B 99 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR B 99 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR B 99 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR B 99 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 99 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 99 " -0.104 2.00e-02 2.50e+03 5.62e-02 6.31e+01 pdb=" CG TYR C 99 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 99 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR C 99 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR C 99 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR C 99 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR C 99 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 99 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 99 " 0.104 2.00e-02 2.50e+03 5.61e-02 6.28e+01 pdb=" CG TYR A 99 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 99 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR A 99 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR A 99 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 99 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 99 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 99 " 0.083 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 6795 2.97 - 3.45: 11904 3.45 - 3.93: 22990 3.93 - 4.42: 26331 4.42 - 4.90: 41881 Nonbonded interactions: 109901 Sorted by model distance: nonbonded pdb=" O LEU L 34 " pdb=" N GLY L 51 " model vdw 2.486 3.120 nonbonded pdb=" O LEU J 34 " pdb=" N GLY J 51 " model vdw 2.487 3.120 nonbonded pdb=" N TYR B 162 " pdb=" O TYR B 162 " model vdw 2.487 2.496 nonbonded pdb=" N TYR A 162 " pdb=" O TYR A 162 " model vdw 2.487 2.496 nonbonded pdb=" N TYR C 162 " pdb=" O TYR C 162 " model vdw 2.487 2.496 ... (remaining 109896 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 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.540 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 : 0.022 0.181 13821 Z= 1.153 Angle : 1.878 12.662 18834 Z= 1.212 Chirality : 0.125 0.525 2166 Planarity : 0.009 0.060 2337 Dihedral : 9.420 79.356 4755 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.55 % Allowed : 1.29 % Favored : 98.16 % Rotamer: Outliers : 0.22 % Allowed : 1.73 % Favored : 98.05 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.57 % 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: 0.66 (0.20), residues: 1629 helix: 1.11 (0.34), residues: 150 sheet: 0.18 (0.20), residues: 591 loop : 0.69 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 77 TYR 0.105 0.012 TYR B 99 PHE 0.019 0.005 PHE H 122 TRP 0.035 0.009 TRP L 36 HIS 0.007 0.003 HIS E 516 Details of bonding type rmsd/Z covalent geometry : bond 0.02208 / 1.14 (13764) covalent geometry : angle 1.85072 / 1.21 (18678) SS BOND : bond 0.01210 / 0.89 ( 15) SS BOND : angle 3.20523 / 1.97 ( 30) hydrogen bonds : bond 0.16687 / 11.29 ( 489) hydrogen bonds : angle 8.08626 / 5.59 ( 1251) link_ALPHA1-3 : bond 0.08211 / 4.78 ( 6) link_ALPHA1-3 : angle 4.43956 / 2.54 ( 18) link_ALPHA1-6 : bond 0.06484 / 3.73 ( 6) link_ALPHA1-6 : angle 3.69408 / 2.13 ( 18) link_BETA1-4 : bond 0.07461 / 4.96 ( 15) link_BETA1-4 : angle 5.47075 / 3.28 ( 45) link_NAG-ASN : bond 0.07781 / 4.98 ( 15) link_NAG-ASN : angle 2.17193 / 1.47 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 402 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7463 (m-10) cc_final: 0.7200 (m-10) REVERT: G 39 TRP cc_start: 0.6928 (m100) cc_final: 0.6167 (m100) REVERT: G 87 GLN cc_start: 0.6231 (tp40) cc_final: 0.5625 (mp10) REVERT: G 130 THR cc_start: 0.6451 (t) cc_final: 0.6235 (m) REVERT: J 32 LYS cc_start: 0.8102 (pttt) cc_final: 0.7769 (mmmt) REVERT: J 59 ILE cc_start: 0.2137 (mm) cc_final: 0.1925 (mm) REVERT: J 61 ASP cc_start: 0.6874 (p0) cc_final: 0.6331 (t70) REVERT: D 510 LYS cc_start: 0.8671 (ptpt) cc_final: 0.7599 (mmtt) REVERT: D 565 THR cc_start: 0.8981 (p) cc_final: 0.8653 (t) REVERT: D 597 TRP cc_start: 0.6151 (m-90) cc_final: 0.5576 (m100) REVERT: B 44 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7641 (mt0) REVERT: B 99 TYR cc_start: 0.7442 (m-10) cc_final: 0.6524 (m-10) REVERT: B 103 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8284 (mt-10) REVERT: B 114 LYS cc_start: 0.8072 (mttm) cc_final: 0.7820 (mttm) REVERT: H 39 TRP cc_start: 0.7228 (m100) cc_final: 0.6314 (m100) REVERT: H 87 GLN cc_start: 0.5715 (tp40) cc_final: 0.5332 (mp10) REVERT: K 61 ASP cc_start: 0.6962 (p0) cc_final: 0.6463 (t70) REVERT: E 510 LYS cc_start: 0.8676 (ptpt) cc_final: 0.7690 (mmtt) REVERT: E 565 THR cc_start: 0.8957 (p) cc_final: 0.8660 (t) REVERT: E 597 TRP cc_start: 0.6119 (m-90) cc_final: 0.5681 (m100) REVERT: C 44 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7811 (mt0) REVERT: C 99 TYR cc_start: 0.7391 (m-10) cc_final: 0.6866 (m-10) REVERT: I 39 TRP cc_start: 0.7103 (m100) cc_final: 0.6151 (m100) REVERT: I 87 GLN cc_start: 0.5745 (tp40) cc_final: 0.5448 (mp10) REVERT: L 32 LYS cc_start: 0.8039 (pttt) cc_final: 0.7787 (ptmm) REVERT: L 33 TYR cc_start: 0.6644 (m-80) cc_final: 0.6412 (m-80) REVERT: L 61 ASP cc_start: 0.6634 (p0) cc_final: 0.6204 (t0) REVERT: L 73 THR cc_start: 0.7689 (m) cc_final: 0.7471 (t) REVERT: L 97 TRP cc_start: 0.6024 (m-10) cc_final: 0.5642 (m-10) REVERT: F 510 LYS cc_start: 0.8658 (ptpt) cc_final: 0.7649 (mmtt) REVERT: F 565 THR cc_start: 0.9049 (p) cc_final: 0.8708 (t) REVERT: F 597 TRP cc_start: 0.5929 (m-90) cc_final: 0.5424 (m100) outliers start: 3 outliers final: 0 residues processed: 402 average time/residue: 0.1172 time to fit residues: 65.0061 Evaluate side-chains 262 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112196 restraints weight = 21258.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.109517 restraints weight = 48495.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110305 restraints weight = 49656.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.111877 restraints weight = 30394.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.111915 restraints weight = 22649.634| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13821 Z= 0.191 Angle : 0.836 18.209 18834 Z= 0.403 Chirality : 0.049 0.266 2166 Planarity : 0.005 0.045 2337 Dihedral : 5.602 22.960 1821 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.96 % Favored : 97.85 % Rotamer: Outliers : 1.73 % Allowed : 9.02 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.21), residues: 1629 helix: 2.60 (0.36), residues: 150 sheet: -0.41 (0.19), residues: 705 loop : 0.59 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 587 TYR 0.021 0.002 TYR I 100 PHE 0.042 0.002 PHE J 72 TRP 0.017 0.002 TRP L 36 HIS 0.003 0.001 HIS E 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (13764) covalent geometry : angle 0.75089 / 0.38 (18678) SS BOND : bond 0.00331 / 0.22 ( 15) SS BOND : angle 1.36059 / 0.88 ( 30) hydrogen bonds : bond 0.05128 / 3.45 ( 489) hydrogen bonds : angle 6.21201 / 4.31 ( 1251) link_ALPHA1-3 : bond 0.01257 / 0.73 ( 6) link_ALPHA1-3 : angle 1.67729 / 0.97 ( 18) link_ALPHA1-6 : bond 0.01105 / 0.61 ( 6) link_ALPHA1-6 : angle 1.61936 / 0.95 ( 18) link_BETA1-4 : bond 0.02061 / 1.66 ( 15) link_BETA1-4 : angle 4.35490 / 2.70 ( 45) link_NAG-ASN : bond 0.01200 / 0.87 ( 15) link_NAG-ASN : angle 6.02732 / 3.73 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 281 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6806 (mp0) REVERT: A 150 ASP cc_start: 0.7631 (m-30) cc_final: 0.7366 (m-30) REVERT: J 80 GLU cc_start: 0.6234 (mm-30) cc_final: 0.5671 (tp30) REVERT: D 510 LYS cc_start: 0.8535 (ptpt) cc_final: 0.7384 (mmtt) REVERT: D 565 THR cc_start: 0.8561 (p) cc_final: 0.8180 (t) REVERT: D 597 TRP cc_start: 0.6308 (m-90) cc_final: 0.5847 (m100) REVERT: H 33 LYS cc_start: 0.5839 (OUTLIER) cc_final: 0.5185 (mptt) REVERT: K 13 LEU cc_start: 0.6769 (mt) cc_final: 0.6524 (mt) REVERT: E 510 LYS cc_start: 0.8623 (ptpt) cc_final: 0.7503 (mmtt) REVERT: E 565 THR cc_start: 0.8753 (p) cc_final: 0.8467 (t) REVERT: E 597 TRP cc_start: 0.6351 (m-90) cc_final: 0.5866 (m100) REVERT: C 100 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6848 (mp0) REVERT: I 53 ARG cc_start: 0.5821 (ttp-170) cc_final: 0.5566 (ptm-80) REVERT: F 510 LYS cc_start: 0.8590 (ptpt) cc_final: 0.7488 (mmtt) REVERT: F 565 THR cc_start: 0.8752 (p) cc_final: 0.8367 (t) REVERT: F 597 TRP cc_start: 0.6214 (m-90) cc_final: 0.5791 (m100) outliers start: 24 outliers final: 18 residues processed: 294 average time/residue: 0.1095 time to fit residues: 45.0793 Evaluate side-chains 264 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 245 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 564 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 59 optimal weight: 0.0570 chunk 73 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 20 optimal weight: 0.0370 chunk 116 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN G 3 GLN D 516 HIS E 516 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS F 595 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121251 restraints weight = 21480.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.120391 restraints weight = 56506.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120102 restraints weight = 50310.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.118928 restraints weight = 39454.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119226 restraints weight = 33774.512| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13821 Z= 0.152 Angle : 0.729 15.714 18834 Z= 0.352 Chirality : 0.045 0.225 2166 Planarity : 0.005 0.046 2337 Dihedral : 5.111 20.642 1821 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.03 % Favored : 97.79 % Rotamer: Outliers : 2.53 % Allowed : 11.69 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.22 (0.21), residues: 1629 helix: 2.50 (0.38), residues: 156 sheet: -0.51 (0.19), residues: 687 loop : 0.50 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 587 TYR 0.028 0.002 TYR K 92 PHE 0.022 0.002 PHE J 72 TRP 0.035 0.002 TRP J 36 HIS 0.007 0.001 HIS J 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (13764) covalent geometry : angle 0.67446 / 0.34 (18678) SS BOND : bond 0.00228 / 0.17 ( 15) SS BOND : angle 1.31422 / 0.85 ( 30) hydrogen bonds : bond 0.04102 / 2.75 ( 489) hydrogen bonds : angle 5.66268 / 3.93 ( 1251) link_ALPHA1-3 : bond 0.01224 / 0.71 ( 6) link_ALPHA1-3 : angle 1.74867 / 1.04 ( 18) link_ALPHA1-6 : bond 0.00711 / 0.41 ( 6) link_ALPHA1-6 : angle 1.53155 / 0.89 ( 18) link_BETA1-4 : bond 0.01875 / 1.52 ( 15) link_BETA1-4 : angle 3.53415 / 2.22 ( 45) link_NAG-ASN : bond 0.00932 / 0.66 ( 15) link_NAG-ASN : angle 4.22482 / 2.29 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: D 510 LYS cc_start: 0.8441 (ptpt) cc_final: 0.7326 (mmtt) REVERT: D 565 THR cc_start: 0.8764 (p) cc_final: 0.8346 (t) REVERT: D 597 TRP cc_start: 0.6245 (m-90) cc_final: 0.5750 (m100) REVERT: K 32 LYS cc_start: 0.8108 (ptmm) cc_final: 0.7833 (mmtt) REVERT: K 92 TYR cc_start: 0.5326 (OUTLIER) cc_final: 0.4562 (m-80) REVERT: K 97 TRP cc_start: 0.5113 (m-90) cc_final: 0.4708 (m-10) REVERT: E 510 LYS cc_start: 0.8572 (ptpt) cc_final: 0.7479 (mmtt) REVERT: E 565 THR cc_start: 0.8787 (p) cc_final: 0.8519 (t) REVERT: E 597 TRP cc_start: 0.6247 (m-90) cc_final: 0.5745 (m100) REVERT: C 184 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8973 (pp) REVERT: C 261 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: F 510 LYS cc_start: 0.8579 (ptpt) cc_final: 0.7395 (mmtt) REVERT: F 551 GLN cc_start: 0.8229 (tp40) cc_final: 0.7855 (tp40) REVERT: F 565 THR cc_start: 0.8865 (p) cc_final: 0.8388 (t) REVERT: F 597 TRP cc_start: 0.6129 (m-90) cc_final: 0.5676 (m100) outliers start: 35 outliers final: 20 residues processed: 284 average time/residue: 0.1054 time to fit residues: 42.2398 Evaluate side-chains 264 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain F residue 545 GLU Chi-restraints excluded: chain F residue 564 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 31 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 0.0370 chunk 156 optimal weight: 0.4980 chunk 131 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 chunk 85 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 144 optimal weight: 0.2980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.145170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121645 restraints weight = 21353.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.120507 restraints weight = 47839.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120851 restraints weight = 41334.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120166 restraints weight = 32274.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119997 restraints weight = 38914.656| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13821 Z= 0.128 Angle : 0.675 12.385 18834 Z= 0.324 Chirality : 0.044 0.200 2166 Planarity : 0.005 0.058 2337 Dihedral : 4.843 20.163 1821 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.97 % Rotamer: Outliers : 2.81 % Allowed : 12.41 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.15 (0.21), residues: 1629 helix: 1.86 (0.39), residues: 174 sheet: -0.62 (0.19), residues: 720 loop : 0.19 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 587 TYR 0.022 0.002 TYR K 92 PHE 0.015 0.001 PHE J 72 TRP 0.018 0.001 TRP I 39 HIS 0.003 0.001 HIS J 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (13764) covalent geometry : angle 0.63335 / 0.31 (18678) SS BOND : bond 0.00169 / 0.12 ( 15) SS BOND : angle 0.82894 / 0.52 ( 30) hydrogen bonds : bond 0.03590 / 2.42 ( 489) hydrogen bonds : angle 5.37129 / 3.73 ( 1251) link_ALPHA1-3 : bond 0.01070 / 0.63 ( 6) link_ALPHA1-3 : angle 1.70731 / 0.99 ( 18) link_ALPHA1-6 : bond 0.00617 / 0.36 ( 6) link_ALPHA1-6 : angle 1.51113 / 0.87 ( 18) link_BETA1-4 : bond 0.01547 / 1.26 ( 15) link_BETA1-4 : angle 3.11599 / 1.97 ( 45) link_NAG-ASN : bond 0.00724 / 0.51 ( 15) link_NAG-ASN : angle 3.42774 / 1.98 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 257 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6724 (mp0) REVERT: D 510 LYS cc_start: 0.8438 (ptpt) cc_final: 0.7295 (mmtt) REVERT: D 565 THR cc_start: 0.8631 (p) cc_final: 0.8328 (t) REVERT: D 597 TRP cc_start: 0.6245 (m-90) cc_final: 0.5854 (m100) REVERT: B 130 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7443 (mtm-85) REVERT: K 92 TYR cc_start: 0.5207 (OUTLIER) cc_final: 0.4544 (m-80) REVERT: K 97 TRP cc_start: 0.5153 (m-90) cc_final: 0.4912 (m-10) REVERT: E 510 LYS cc_start: 0.8555 (ptpt) cc_final: 0.7392 (mmtt) REVERT: E 565 THR cc_start: 0.8793 (p) cc_final: 0.8457 (t) REVERT: C 261 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: F 510 LYS cc_start: 0.8539 (ptpt) cc_final: 0.7284 (mmtt) REVERT: F 551 GLN cc_start: 0.8077 (tp40) cc_final: 0.7817 (tp40) REVERT: F 565 THR cc_start: 0.8808 (p) cc_final: 0.8443 (t) REVERT: F 578 GLU cc_start: 0.7561 (tt0) cc_final: 0.7238 (tt0) REVERT: F 597 TRP cc_start: 0.6115 (m-90) cc_final: 0.5732 (m100) outliers start: 39 outliers final: 26 residues processed: 277 average time/residue: 0.1050 time to fit residues: 41.6611 Evaluate side-chains 269 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 564 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 82 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 136 optimal weight: 0.0040 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 43 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119788 restraints weight = 21475.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118400 restraints weight = 57325.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118320 restraints weight = 51045.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117183 restraints weight = 38701.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117489 restraints weight = 33160.840| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13821 Z= 0.138 Angle : 0.670 12.564 18834 Z= 0.321 Chirality : 0.044 0.175 2166 Planarity : 0.005 0.062 2337 Dihedral : 4.755 19.561 1821 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.21 % Favored : 97.54 % Rotamer: Outliers : 3.17 % Allowed : 13.42 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.17 (0.21), residues: 1629 helix: 1.89 (0.38), residues: 174 sheet: -0.72 (0.19), residues: 708 loop : 0.25 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 587 TYR 0.029 0.002 TYR H 85 PHE 0.013 0.001 PHE G 113 TRP 0.025 0.002 TRP G 39 HIS 0.003 0.001 HIS J 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (13764) covalent geometry : angle 0.63605 / 0.31 (18678) SS BOND : bond 0.00175 / 0.13 ( 15) SS BOND : angle 0.87318 / 0.57 ( 30) hydrogen bonds : bond 0.03561 / 2.40 ( 489) hydrogen bonds : angle 5.22114 / 3.65 ( 1251) link_ALPHA1-3 : bond 0.01046 / 0.61 ( 6) link_ALPHA1-3 : angle 1.75529 / 1.02 ( 18) link_ALPHA1-6 : bond 0.00587 / 0.34 ( 6) link_ALPHA1-6 : angle 1.51958 / 0.88 ( 18) link_BETA1-4 : bond 0.01411 / 1.16 ( 15) link_BETA1-4 : angle 2.97331 / 1.88 ( 45) link_NAG-ASN : bond 0.00573 / 0.40 ( 15) link_NAG-ASN : angle 2.86965 / 1.71 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 251 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 510 LYS cc_start: 0.8436 (ptpt) cc_final: 0.7261 (mmtt) REVERT: D 551 GLN cc_start: 0.8102 (tp40) cc_final: 0.7531 (tp40) REVERT: D 565 THR cc_start: 0.8659 (p) cc_final: 0.8397 (t) REVERT: D 597 TRP cc_start: 0.6323 (m-90) cc_final: 0.5927 (m100) REVERT: B 130 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7260 (mtm-85) REVERT: B 261 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: K 86 VAL cc_start: 0.7177 (OUTLIER) cc_final: 0.6873 (p) REVERT: K 92 TYR cc_start: 0.5492 (OUTLIER) cc_final: 0.4671 (m-80) REVERT: K 97 TRP cc_start: 0.5472 (m-90) cc_final: 0.4982 (m-10) REVERT: E 510 LYS cc_start: 0.8571 (ptpt) cc_final: 0.7320 (mmtt) REVERT: E 565 THR cc_start: 0.8699 (p) cc_final: 0.8469 (t) REVERT: C 184 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8873 (pp) REVERT: C 261 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: F 510 LYS cc_start: 0.8559 (ptpt) cc_final: 0.7251 (mmtt) REVERT: F 565 THR cc_start: 0.8867 (p) cc_final: 0.8507 (t) REVERT: F 578 GLU cc_start: 0.7537 (tt0) cc_final: 0.7271 (tt0) REVERT: F 597 TRP cc_start: 0.6209 (m-90) cc_final: 0.5839 (m100) outliers start: 44 outliers final: 30 residues processed: 274 average time/residue: 0.1072 time to fit residues: 41.9504 Evaluate side-chains 276 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 564 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 55 optimal weight: 0.0570 chunk 154 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.141418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108791 restraints weight = 21569.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.101681 restraints weight = 24837.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.102006 restraints weight = 32934.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.102693 restraints weight = 25022.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102867 restraints weight = 21884.135| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13821 Z= 0.180 Angle : 0.694 14.354 18834 Z= 0.332 Chirality : 0.045 0.201 2166 Planarity : 0.005 0.065 2337 Dihedral : 4.802 21.926 1821 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.52 % Favored : 97.18 % Rotamer: Outliers : 3.17 % Allowed : 13.78 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.28 (0.21), residues: 1629 helix: 1.81 (0.39), residues: 174 sheet: -0.61 (0.19), residues: 678 loop : -0.07 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 587 TYR 0.021 0.002 TYR I 100 PHE 0.032 0.002 PHE E 592 TRP 0.030 0.002 TRP K 36 HIS 0.003 0.001 HIS D 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (13764) covalent geometry : angle 0.66543 / 0.33 (18678) SS BOND : bond 0.00263 / 0.20 ( 15) SS BOND : angle 0.98283 / 0.61 ( 30) hydrogen bonds : bond 0.03963 / 2.68 ( 489) hydrogen bonds : angle 5.13806 / 3.59 ( 1251) link_ALPHA1-3 : bond 0.00983 / 0.58 ( 6) link_ALPHA1-3 : angle 1.76787 / 1.03 ( 18) link_ALPHA1-6 : bond 0.00508 / 0.30 ( 6) link_ALPHA1-6 : angle 1.52598 / 0.88 ( 18) link_BETA1-4 : bond 0.01358 / 1.13 ( 15) link_BETA1-4 : angle 2.94332 / 1.86 ( 45) link_NAG-ASN : bond 0.00485 / 0.32 ( 15) link_NAG-ASN : angle 2.49530 / 1.58 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6900 (mp0) REVERT: G 33 LYS cc_start: 0.5715 (OUTLIER) cc_final: 0.4803 (mttt) REVERT: D 510 LYS cc_start: 0.8548 (ptpt) cc_final: 0.7253 (mmtt) REVERT: D 551 GLN cc_start: 0.8125 (tp40) cc_final: 0.7571 (tp40) REVERT: D 565 THR cc_start: 0.8515 (p) cc_final: 0.8217 (t) REVERT: D 597 TRP cc_start: 0.6362 (m-90) cc_final: 0.5933 (m100) REVERT: B 184 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8813 (pp) REVERT: B 261 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: E 510 LYS cc_start: 0.8668 (ptpt) cc_final: 0.7315 (mmtt) REVERT: E 551 GLN cc_start: 0.8247 (tp40) cc_final: 0.7790 (tp40) REVERT: E 565 THR cc_start: 0.8604 (p) cc_final: 0.8403 (t) REVERT: E 597 TRP cc_start: 0.6325 (m-90) cc_final: 0.5872 (m100) REVERT: C 184 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8921 (pp) REVERT: C 261 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: F 510 LYS cc_start: 0.8544 (ptpt) cc_final: 0.7145 (mmtt) REVERT: F 565 THR cc_start: 0.8703 (p) cc_final: 0.8358 (t) REVERT: F 578 GLU cc_start: 0.7508 (tt0) cc_final: 0.7269 (tt0) REVERT: F 597 TRP cc_start: 0.6267 (m-90) cc_final: 0.5768 (m100) outliers start: 44 outliers final: 33 residues processed: 273 average time/residue: 0.1059 time to fit residues: 41.4700 Evaluate side-chains 278 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 564 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 160 optimal weight: 0.5980 chunk 23 optimal weight: 30.0000 chunk 138 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN H 42 GLN K 39 GLN ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.142420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111268 restraints weight = 21390.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.102905 restraints weight = 25902.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103364 restraints weight = 39385.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104588 restraints weight = 28641.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104904 restraints weight = 22719.805| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13821 Z= 0.139 Angle : 0.658 10.481 18834 Z= 0.320 Chirality : 0.044 0.176 2166 Planarity : 0.005 0.065 2337 Dihedral : 4.662 19.405 1821 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.27 % Favored : 97.36 % Rotamer: Outliers : 2.96 % Allowed : 14.94 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.21), residues: 1629 helix: 1.89 (0.39), residues: 174 sheet: -0.61 (0.19), residues: 678 loop : -0.11 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 587 TYR 0.028 0.001 TYR H 85 PHE 0.012 0.001 PHE G 113 TRP 0.032 0.002 TRP K 97 HIS 0.004 0.001 HIS K 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (13764) covalent geometry : angle 0.63338 / 0.31 (18678) SS BOND : bond 0.00165 / 0.13 ( 15) SS BOND : angle 0.81385 / 0.52 ( 30) hydrogen bonds : bond 0.03517 / 2.39 ( 489) hydrogen bonds : angle 5.05526 / 3.53 ( 1251) link_ALPHA1-3 : bond 0.00998 / 0.59 ( 6) link_ALPHA1-3 : angle 1.76539 / 1.03 ( 18) link_ALPHA1-6 : bond 0.00546 / 0.31 ( 6) link_ALPHA1-6 : angle 1.49893 / 0.87 ( 18) link_BETA1-4 : bond 0.01367 / 1.12 ( 15) link_BETA1-4 : angle 2.80721 / 1.79 ( 45) link_NAG-ASN : bond 0.00415 / 0.29 ( 15) link_NAG-ASN : angle 2.10799 / 1.33 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 246 time to evaluate : 0.418 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: A 100 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6984 (mp0) REVERT: G 33 LYS cc_start: 0.5771 (OUTLIER) cc_final: 0.4965 (mttm) REVERT: G 54 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6631 (tt) REVERT: D 510 LYS cc_start: 0.8521 (ptpt) cc_final: 0.7191 (mmtt) REVERT: D 551 GLN cc_start: 0.8142 (tp40) cc_final: 0.7593 (tp40) REVERT: D 565 THR cc_start: 0.8524 (p) cc_final: 0.8267 (t) REVERT: D 597 TRP cc_start: 0.6420 (m-90) cc_final: 0.6008 (m100) REVERT: B 231 GLU cc_start: 0.7013 (mp0) cc_final: 0.6515 (mp0) REVERT: K 91 GLN cc_start: 0.6598 (pp30) cc_final: 0.5787 (pp30) REVERT: K 92 TYR cc_start: 0.5492 (OUTLIER) cc_final: 0.4798 (m-80) REVERT: E 510 LYS cc_start: 0.8664 (ptpt) cc_final: 0.7319 (mmtt) REVERT: E 587 ARG cc_start: 0.7892 (ttm110) cc_final: 0.7663 (mtp-110) REVERT: C 184 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8833 (pp) REVERT: C 261 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.8221 (m-80) REVERT: C 265 LYS cc_start: 0.8675 (mttt) cc_final: 0.8401 (mttt) REVERT: F 510 LYS cc_start: 0.8523 (ptpt) cc_final: 0.7095 (mmtt) REVERT: F 551 GLN cc_start: 0.8134 (tp40) cc_final: 0.7895 (tp40) REVERT: F 565 THR cc_start: 0.8768 (p) cc_final: 0.8420 (t) REVERT: F 578 GLU cc_start: 0.7521 (tt0) cc_final: 0.7258 (tt0) REVERT: F 597 TRP cc_start: 0.6312 (m-90) cc_final: 0.5885 (m100) outliers start: 41 outliers final: 30 residues processed: 270 average time/residue: 0.1189 time to fit residues: 45.7953 Evaluate side-chains 269 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 564 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 87 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 24 optimal weight: 20.0000 chunk 93 optimal weight: 0.0010 chunk 50 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN C 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118396 restraints weight = 21347.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118494 restraints weight = 57191.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117613 restraints weight = 45190.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116680 restraints weight = 39328.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116936 restraints weight = 29203.610| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13821 Z= 0.149 Angle : 0.671 10.894 18834 Z= 0.321 Chirality : 0.044 0.210 2166 Planarity : 0.005 0.068 2337 Dihedral : 4.614 20.981 1821 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.89 % Favored : 96.75 % Rotamer: Outliers : 3.03 % Allowed : 15.08 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.36 (0.21), residues: 1629 helix: 1.69 (0.39), residues: 180 sheet: -0.63 (0.20), residues: 657 loop : -0.19 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 587 TYR 0.021 0.001 TYR J 50 PHE 0.024 0.001 PHE E 592 TRP 0.017 0.001 TRP L 97 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (13764) covalent geometry : angle 0.63912 / 0.31 (18678) SS BOND : bond 0.00210 / 0.17 ( 15) SS BOND : angle 0.84694 / 0.54 ( 30) hydrogen bonds : bond 0.03582 / 2.42 ( 489) hydrogen bonds : angle 4.97745 / 3.51 ( 1251) link_ALPHA1-3 : bond 0.00945 / 0.56 ( 6) link_ALPHA1-3 : angle 1.78188 / 1.04 ( 18) link_ALPHA1-6 : bond 0.00535 / 0.31 ( 6) link_ALPHA1-6 : angle 1.47498 / 0.86 ( 18) link_BETA1-4 : bond 0.01301 / 1.07 ( 15) link_BETA1-4 : angle 2.75101 / 1.76 ( 45) link_NAG-ASN : bond 0.00469 / 0.28 ( 15) link_NAG-ASN : angle 2.91937 / 2.16 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 0.331 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: A 99 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6220 (m-10) REVERT: A 100 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6949 (mp0) REVERT: G 33 LYS cc_start: 0.5765 (OUTLIER) cc_final: 0.4972 (mttm) REVERT: G 54 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.6677 (tt) REVERT: D 510 LYS cc_start: 0.8544 (ptpt) cc_final: 0.7204 (mmtt) REVERT: D 565 THR cc_start: 0.8597 (p) cc_final: 0.8292 (t) REVERT: D 597 TRP cc_start: 0.6412 (m-90) cc_final: 0.5968 (m100) REVERT: B 231 GLU cc_start: 0.7103 (mp0) cc_final: 0.6613 (mp0) REVERT: K 91 GLN cc_start: 0.5639 (pp30) cc_final: 0.5362 (pp30) REVERT: K 92 TYR cc_start: 0.5231 (OUTLIER) cc_final: 0.4501 (m-80) REVERT: E 510 LYS cc_start: 0.8655 (ptpt) cc_final: 0.7302 (mmtt) REVERT: E 558 LEU cc_start: 0.8699 (tp) cc_final: 0.8379 (mt) REVERT: E 597 TRP cc_start: 0.6375 (m-90) cc_final: 0.5959 (m100) REVERT: C 99 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.6099 (m-10) REVERT: C 184 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8858 (pp) REVERT: C 265 LYS cc_start: 0.8664 (mttt) cc_final: 0.8419 (mttt) REVERT: F 510 LYS cc_start: 0.8541 (ptpt) cc_final: 0.7163 (mmtt) REVERT: F 551 GLN cc_start: 0.8131 (tp40) cc_final: 0.7908 (tp40) REVERT: F 565 THR cc_start: 0.8802 (p) cc_final: 0.8436 (t) REVERT: F 578 GLU cc_start: 0.7536 (tt0) cc_final: 0.7257 (tt0) REVERT: F 597 TRP cc_start: 0.6345 (m-90) cc_final: 0.5839 (m100) outliers start: 42 outliers final: 29 residues processed: 271 average time/residue: 0.1095 time to fit residues: 42.1095 Evaluate side-chains 274 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain F residue 558 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 86 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN C 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117072 restraints weight = 21863.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116104 restraints weight = 62444.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.114068 restraints weight = 45464.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113256 restraints weight = 43967.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113557 restraints weight = 28138.151| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13821 Z= 0.242 Angle : 0.770 19.325 18834 Z= 0.366 Chirality : 0.048 0.573 2166 Planarity : 0.005 0.070 2337 Dihedral : 4.919 22.085 1821 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.19 % Favored : 96.50 % Rotamer: Outliers : 3.17 % Allowed : 15.58 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.61 (0.21), residues: 1629 helix: 1.40 (0.39), residues: 180 sheet: -0.80 (0.20), residues: 657 loop : -0.31 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 587 TYR 0.022 0.002 TYR H 100 PHE 0.026 0.002 PHE J 72 TRP 0.030 0.002 TRP G 39 HIS 0.004 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.24 (13764) covalent geometry : angle 0.72623 / 0.36 (18678) SS BOND : bond 0.00344 / 0.25 ( 15) SS BOND : angle 1.01019 / 0.66 ( 30) hydrogen bonds : bond 0.04376 / 2.96 ( 489) hydrogen bonds : angle 5.09456 / 3.60 ( 1251) link_ALPHA1-3 : bond 0.00931 / 0.55 ( 6) link_ALPHA1-3 : angle 1.82586 / 1.07 ( 18) link_ALPHA1-6 : bond 0.00412 / 0.24 ( 6) link_ALPHA1-6 : angle 1.49840 / 0.87 ( 18) link_BETA1-4 : bond 0.01278 / 1.07 ( 15) link_BETA1-4 : angle 2.94258 / 1.86 ( 45) link_NAG-ASN : bond 0.00461 / 0.31 ( 15) link_NAG-ASN : angle 4.18366 / 3.46 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 0.372 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: A 99 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.6546 (m-10) REVERT: A 100 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7167 (mp0) REVERT: G 33 LYS cc_start: 0.5816 (OUTLIER) cc_final: 0.4973 (mttm) REVERT: G 54 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6936 (tt) REVERT: D 510 LYS cc_start: 0.8643 (ptpt) cc_final: 0.7227 (mmtt) REVERT: D 565 THR cc_start: 0.8538 (p) cc_final: 0.8225 (t) REVERT: D 597 TRP cc_start: 0.6489 (m-90) cc_final: 0.6070 (m100) REVERT: B 130 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7248 (mtm-85) REVERT: B 231 GLU cc_start: 0.7124 (mp0) cc_final: 0.6815 (mp0) REVERT: K 92 TYR cc_start: 0.5300 (OUTLIER) cc_final: 0.4784 (m-80) REVERT: E 510 LYS cc_start: 0.8730 (ptpt) cc_final: 0.7356 (mmtt) REVERT: E 551 GLN cc_start: 0.8387 (tp40) cc_final: 0.7979 (tp40) REVERT: E 597 TRP cc_start: 0.6490 (m-90) cc_final: 0.6086 (m100) REVERT: C 99 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.5966 (m-10) REVERT: F 510 LYS cc_start: 0.8596 (ptpt) cc_final: 0.7201 (mmtt) REVERT: F 565 THR cc_start: 0.8720 (p) cc_final: 0.8317 (t) REVERT: F 578 GLU cc_start: 0.7571 (tt0) cc_final: 0.7296 (tt0) REVERT: F 597 TRP cc_start: 0.6295 (m-90) cc_final: 0.5862 (m100) outliers start: 44 outliers final: 30 residues processed: 272 average time/residue: 0.1131 time to fit residues: 43.3878 Evaluate side-chains 272 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 32 LYS Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 577 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 89 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 145 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 150 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.140968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118271 restraints weight = 21397.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117366 restraints weight = 62191.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115184 restraints weight = 41740.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113491 restraints weight = 48787.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113802 restraints weight = 36496.237| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13821 Z= 0.146 Angle : 0.701 16.843 18834 Z= 0.337 Chirality : 0.046 0.462 2166 Planarity : 0.005 0.070 2337 Dihedral : 4.791 21.480 1821 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.95 % Favored : 96.75 % Rotamer: Outliers : 2.60 % Allowed : 16.16 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.54 (0.21), residues: 1629 helix: 1.67 (0.40), residues: 180 sheet: -0.79 (0.20), residues: 660 loop : -0.30 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 587 TYR 0.022 0.002 TYR J 50 PHE 0.031 0.001 PHE J 72 TRP 0.030 0.002 TRP G 39 HIS 0.004 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (13764) covalent geometry : angle 0.66251 / 0.33 (18678) SS BOND : bond 0.00192 / 0.15 ( 15) SS BOND : angle 0.81894 / 0.53 ( 30) hydrogen bonds : bond 0.03648 / 2.47 ( 489) hydrogen bonds : angle 5.02373 / 3.55 ( 1251) link_ALPHA1-3 : bond 0.00945 / 0.57 ( 6) link_ALPHA1-3 : angle 1.76516 / 1.03 ( 18) link_ALPHA1-6 : bond 0.00553 / 0.31 ( 6) link_ALPHA1-6 : angle 1.48486 / 0.87 ( 18) link_BETA1-4 : bond 0.01384 / 1.14 ( 15) link_BETA1-4 : angle 2.77742 / 1.77 ( 45) link_NAG-ASN : bond 0.00342 / 0.22 ( 15) link_NAG-ASN : angle 3.61830 / 2.98 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.496 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: A 99 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6264 (m-10) REVERT: A 100 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6981 (mp0) REVERT: G 33 LYS cc_start: 0.5864 (OUTLIER) cc_final: 0.4894 (mttm) REVERT: G 54 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6850 (tt) REVERT: D 510 LYS cc_start: 0.8544 (ptpt) cc_final: 0.7206 (mmtt) REVERT: D 551 GLN cc_start: 0.8172 (tp40) cc_final: 0.7964 (tp40) REVERT: D 565 THR cc_start: 0.8498 (p) cc_final: 0.8234 (t) REVERT: D 597 TRP cc_start: 0.6466 (m-90) cc_final: 0.6051 (m100) REVERT: B 231 GLU cc_start: 0.7101 (mp0) cc_final: 0.6705 (mp0) REVERT: K 92 TYR cc_start: 0.5367 (OUTLIER) cc_final: 0.4949 (m-80) REVERT: E 510 LYS cc_start: 0.8671 (ptpt) cc_final: 0.7314 (mmtt) REVERT: E 551 GLN cc_start: 0.8374 (tp40) cc_final: 0.7960 (tp40) REVERT: E 597 TRP cc_start: 0.6401 (m-90) cc_final: 0.5998 (m100) REVERT: C 99 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.5947 (m-10) REVERT: C 265 LYS cc_start: 0.8387 (mttm) cc_final: 0.8107 (mttt) REVERT: F 510 LYS cc_start: 0.8532 (ptpt) cc_final: 0.7136 (mmtt) REVERT: F 565 THR cc_start: 0.8697 (p) cc_final: 0.8306 (t) REVERT: F 578 GLU cc_start: 0.7431 (tt0) cc_final: 0.7176 (tt0) REVERT: F 597 TRP cc_start: 0.6218 (m-90) cc_final: 0.5761 (m100) outliers start: 36 outliers final: 25 residues processed: 270 average time/residue: 0.1156 time to fit residues: 44.6533 Evaluate side-chains 267 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 32 LYS Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 577 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 31 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 155 optimal weight: 0.0970 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN C 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110779 restraints weight = 21592.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.103092 restraints weight = 24909.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.103579 restraints weight = 41678.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.105189 restraints weight = 29107.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.105301 restraints weight = 21329.844| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13821 Z= 0.137 Angle : 0.696 13.863 18834 Z= 0.333 Chirality : 0.045 0.351 2166 Planarity : 0.005 0.067 2337 Dihedral : 4.671 20.811 1821 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.25 % Favored : 96.44 % Rotamer: Outliers : 2.31 % Allowed : 16.59 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.49 (0.21), residues: 1629 helix: 1.76 (0.40), residues: 180 sheet: -0.75 (0.20), residues: 657 loop : -0.29 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 587 TYR 0.021 0.001 TYR L 50 PHE 0.032 0.001 PHE G 113 TRP 0.048 0.002 TRP I 39 HIS 0.004 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (13764) covalent geometry : angle 0.66393 / 0.33 (18678) SS BOND : bond 0.00220 / 0.15 ( 15) SS BOND : angle 0.92447 / 0.61 ( 30) hydrogen bonds : bond 0.03433 / 2.32 ( 489) hydrogen bonds : angle 4.94780 / 3.51 ( 1251) link_ALPHA1-3 : bond 0.00945 / 0.56 ( 6) link_ALPHA1-3 : angle 1.78218 / 1.04 ( 18) link_ALPHA1-6 : bond 0.00493 / 0.29 ( 6) link_ALPHA1-6 : angle 1.44274 / 0.85 ( 18) link_BETA1-4 : bond 0.01349 / 1.11 ( 15) link_BETA1-4 : angle 2.69247 / 1.72 ( 45) link_NAG-ASN : bond 0.00321 / 0.22 ( 15) link_NAG-ASN : angle 3.09545 / 2.48 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1844.00 seconds wall clock time: 32 minutes 53.04 seconds (1973.04 seconds total)