Starting phenix.real_space_refine on Wed Mar 4 12:30:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kfb_22848/03_2026/7kfb_22848.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kfb_22848/03_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_22848/03_2026/7kfb_22848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kfb_22848/03_2026/7kfb_22848.map" model { file = "/net/cci-nas-00/data/ceres_data/7kfb_22848/03_2026/7kfb_22848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kfb_22848/03_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-5986/lib/python3.9/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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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: 2.32, 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: 1.23 Conformation dependent library (CDL) restraints added in 564.5 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: 0.59 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: 2.37 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 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 - 21.39: 8322 21.39 - 42.78: 183 42.78 - 64.16: 54 64.16 - 85.55: 45 85.55 - 106.94: 24 Dihedral angle restraints: 8628 sinusoidal: 3918 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 8625 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: 0.03 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: 2.030 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.460 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 13.131 106.938 5601 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 covalent geometry : bond 0.02208 (13764) covalent geometry : angle 1.85072 (18678) SS BOND : bond 0.01210 ( 15) SS BOND : angle 3.20523 ( 30) hydrogen bonds : bond 0.16687 ( 489) hydrogen bonds : angle 8.08626 ( 1251) link_ALPHA1-3 : bond 0.08211 ( 6) link_ALPHA1-3 : angle 4.43956 ( 18) link_ALPHA1-6 : bond 0.06484 ( 6) link_ALPHA1-6 : angle 3.69408 ( 18) link_BETA1-4 : bond 0.07461 ( 15) link_BETA1-4 : angle 5.47075 ( 45) link_NAG-ASN : bond 0.07781 ( 15) link_NAG-ASN : angle 2.17193 ( 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 : 0.425 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: 0.1382 time to fit residues: 75.8890 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 : 0.499 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.145428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115084 restraints weight = 21270.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.113501 restraints weight = 54320.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113442 restraints weight = 46907.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.113007 restraints weight = 29408.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113491 restraints weight = 25612.456| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13821 Z= 0.193 Angle : 0.844 19.094 18834 Z= 0.407 Chirality : 0.050 0.266 2166 Planarity : 0.005 0.044 2337 Dihedral : 12.647 90.215 2667 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.96 % Favored : 97.85 % Rotamer: Outliers : 1.59 % Allowed : 9.31 % Favored : 89.11 % 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: 0.36 (0.21), residues: 1629 helix: 2.69 (0.37), residues: 147 sheet: -0.39 (0.19), residues: 687 loop : 0.57 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 587 TYR 0.022 0.002 TYR H 118 PHE 0.041 0.002 PHE J 72 TRP 0.021 0.002 TRP L 36 HIS 0.003 0.001 HIS E 549 Details of bonding type rmsd covalent geometry : bond 0.00426 (13764) covalent geometry : angle 0.75440 (18678) SS BOND : bond 0.00381 ( 15) SS BOND : angle 1.39131 ( 30) hydrogen bonds : bond 0.05146 ( 489) hydrogen bonds : angle 6.19541 ( 1251) link_ALPHA1-3 : bond 0.01582 ( 6) link_ALPHA1-3 : angle 0.84606 ( 18) link_ALPHA1-6 : bond 0.00989 ( 6) link_ALPHA1-6 : angle 1.80918 ( 18) link_BETA1-4 : bond 0.02071 ( 15) link_BETA1-4 : angle 4.54033 ( 45) link_NAG-ASN : bond 0.01029 ( 15) link_NAG-ASN : angle 6.17951 ( 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 304 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 282 time to evaluate : 0.420 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: 0.7147 (mt-10) cc_final: 0.6808 (mp0) REVERT: A 150 ASP cc_start: 0.7650 (m-30) cc_final: 0.7398 (m-30) REVERT: J 80 GLU cc_start: 0.6151 (mm-30) cc_final: 0.5698 (tp30) REVERT: D 510 LYS cc_start: 0.8522 (ptpt) cc_final: 0.7389 (mmtt) REVERT: D 565 THR cc_start: 0.8603 (p) cc_final: 0.8209 (t) REVERT: D 597 TRP cc_start: 0.6313 (m-90) cc_final: 0.5858 (m100) REVERT: H 33 LYS cc_start: 0.5836 (OUTLIER) cc_final: 0.5168 (mptt) REVERT: E 510 LYS cc_start: 0.8622 (ptpt) cc_final: 0.7503 (mmtt) REVERT: E 565 THR cc_start: 0.8796 (p) cc_final: 0.8480 (t) REVERT: E 578 GLU cc_start: 0.7500 (tt0) cc_final: 0.7299 (tt0) REVERT: E 597 TRP cc_start: 0.6374 (m-90) cc_final: 0.5891 (m100) REVERT: C 100 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6781 (mp0) REVERT: I 53 ARG cc_start: 0.5759 (ttp-170) cc_final: 0.5492 (ptm-80) REVERT: F 510 LYS cc_start: 0.8597 (ptpt) cc_final: 0.7504 (mmtt) REVERT: F 565 THR cc_start: 0.8768 (p) cc_final: 0.8375 (t) REVERT: F 597 TRP cc_start: 0.6248 (m-90) cc_final: 0.5824 (m100) outliers start: 22 outliers final: 17 residues processed: 295 average time/residue: 0.1315 time to fit residues: 54.3160 Evaluate side-chains 263 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 245 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 59 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN G 3 GLN D 516 HIS E 516 HIS E 595 GLN ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS F 595 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119248 restraints weight = 21524.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118583 restraints weight = 53724.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118283 restraints weight = 50076.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117322 restraints weight = 38405.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117571 restraints weight = 33563.283| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13821 Z= 0.168 Angle : 0.746 16.102 18834 Z= 0.358 Chirality : 0.047 0.222 2166 Planarity : 0.005 0.045 2337 Dihedral : 11.463 83.823 2667 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.09 % Favored : 97.73 % Rotamer: Outliers : 2.74 % Allowed : 11.69 % Favored : 85.57 % 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: 0.16 (0.21), residues: 1629 helix: 2.43 (0.38), residues: 156 sheet: -0.58 (0.19), residues: 702 loop : 0.52 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 587 TYR 0.026 0.002 TYR K 92 PHE 0.023 0.002 PHE K 99 TRP 0.031 0.002 TRP J 36 HIS 0.006 0.001 HIS J 90 Details of bonding type rmsd covalent geometry : bond 0.00372 (13764) covalent geometry : angle 0.68564 (18678) SS BOND : bond 0.00341 ( 15) SS BOND : angle 1.37245 ( 30) hydrogen bonds : bond 0.04300 ( 489) hydrogen bonds : angle 5.69539 ( 1251) link_ALPHA1-3 : bond 0.01723 ( 6) link_ALPHA1-3 : angle 0.96949 ( 18) link_ALPHA1-6 : bond 0.00945 ( 6) link_ALPHA1-6 : angle 1.84750 ( 18) link_BETA1-4 : bond 0.01829 ( 15) link_BETA1-4 : angle 3.80541 ( 45) link_NAG-ASN : bond 0.00887 ( 15) link_NAG-ASN : angle 4.48062 ( 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 307 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.486 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: 0.7049 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: G 33 LYS cc_start: 0.5816 (OUTLIER) cc_final: 0.4874 (mttt) REVERT: D 510 LYS cc_start: 0.8478 (ptpt) cc_final: 0.7348 (mmtt) REVERT: D 565 THR cc_start: 0.8751 (p) cc_final: 0.8336 (t) REVERT: D 597 TRP cc_start: 0.6281 (m-90) cc_final: 0.5774 (m100) REVERT: B 130 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7431 (mtm-85) REVERT: K 32 LYS cc_start: 0.8108 (ptmm) cc_final: 0.7828 (mmtt) REVERT: K 92 TYR cc_start: 0.5251 (OUTLIER) cc_final: 0.4584 (m-80) REVERT: K 97 TRP cc_start: 0.5195 (m-90) cc_final: 0.4763 (m-10) REVERT: E 510 LYS cc_start: 0.8614 (ptpt) cc_final: 0.7487 (mmtt) REVERT: E 565 THR cc_start: 0.8794 (p) cc_final: 0.8509 (t) REVERT: E 597 TRP cc_start: 0.6284 (m-90) cc_final: 0.5781 (m100) REVERT: C 184 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8997 (pp) REVERT: C 261 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7475 (m-80) REVERT: F 510 LYS cc_start: 0.8596 (ptpt) cc_final: 0.7386 (mmtt) REVERT: F 551 GLN cc_start: 0.8231 (tp40) cc_final: 0.7852 (tp40) REVERT: F 565 THR cc_start: 0.8876 (p) cc_final: 0.8411 (t) REVERT: F 597 TRP cc_start: 0.6177 (m-90) cc_final: 0.5731 (m100) outliers start: 38 outliers final: 24 residues processed: 289 average time/residue: 0.1307 time to fit residues: 52.4247 Evaluate side-chains 275 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain G residue 33 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 D residue 544 THR Chi-restraints excluded: chain D residue 545 GLU 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 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 L residue 79 LEU 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: 9.9990 chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 131 optimal weight: 0.0060 chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 20 optimal weight: 0.0970 chunk 144 optimal weight: 6.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.142748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108705 restraints weight = 21390.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.102158 restraints weight = 27023.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.102823 restraints weight = 49531.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.104321 restraints weight = 30719.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.104505 restraints weight = 24237.349| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13821 Z= 0.170 Angle : 0.721 12.857 18834 Z= 0.343 Chirality : 0.047 0.261 2166 Planarity : 0.005 0.069 2337 Dihedral : 10.558 78.130 2667 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.09 % Favored : 97.73 % Rotamer: Outliers : 3.10 % Allowed : 12.41 % Favored : 84.49 % 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: -0.13 (0.21), residues: 1629 helix: 1.64 (0.39), residues: 174 sheet: -0.69 (0.19), residues: 693 loop : 0.33 (0.23), residues: 762 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 0.002 PHE J 72 TRP 0.017 0.002 TRP I 39 HIS 0.003 0.001 HIS D 549 Details of bonding type rmsd covalent geometry : bond 0.00385 (13764) covalent geometry : angle 0.67634 (18678) SS BOND : bond 0.00238 ( 15) SS BOND : angle 0.94961 ( 30) hydrogen bonds : bond 0.04028 ( 489) hydrogen bonds : angle 5.43774 ( 1251) link_ALPHA1-3 : bond 0.01584 ( 6) link_ALPHA1-3 : angle 1.04834 ( 18) link_ALPHA1-6 : bond 0.00983 ( 6) link_ALPHA1-6 : angle 1.96608 ( 18) link_BETA1-4 : bond 0.01608 ( 15) link_BETA1-4 : angle 3.45290 ( 45) link_NAG-ASN : bond 0.00678 ( 15) link_NAG-ASN : angle 3.65303 ( 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 294 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 0.509 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: 0.7165 (mt-10) cc_final: 0.6891 (mp0) REVERT: J 32 LYS cc_start: 0.8930 (pttt) cc_final: 0.8244 (mmtt) REVERT: D 510 LYS cc_start: 0.8500 (ptpt) cc_final: 0.7274 (mmtt) REVERT: D 565 THR cc_start: 0.8565 (p) cc_final: 0.8200 (t) REVERT: D 597 TRP cc_start: 0.6283 (m-90) cc_final: 0.5858 (m100) REVERT: B 130 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7338 (mtm-85) REVERT: B 261 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: K 32 LYS cc_start: 0.8561 (ptmm) cc_final: 0.7953 (mmtt) REVERT: K 92 TYR cc_start: 0.5640 (OUTLIER) cc_final: 0.4780 (m-80) REVERT: K 97 TRP cc_start: 0.5865 (m-90) cc_final: 0.4913 (m-10) REVERT: E 510 LYS cc_start: 0.8637 (ptpt) cc_final: 0.7359 (mmtt) REVERT: E 565 THR cc_start: 0.8650 (p) cc_final: 0.8382 (t) REVERT: E 597 TRP cc_start: 0.6291 (m-90) cc_final: 0.5886 (m100) REVERT: C 184 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8966 (pp) REVERT: C 261 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: F 510 LYS cc_start: 0.8590 (ptpt) cc_final: 0.7296 (mmtt) REVERT: F 551 GLN cc_start: 0.8111 (tp40) cc_final: 0.7865 (tp40) REVERT: F 565 THR cc_start: 0.8716 (p) cc_final: 0.8335 (t) REVERT: F 578 GLU cc_start: 0.7684 (tt0) cc_final: 0.7379 (tt0) REVERT: F 597 TRP cc_start: 0.6205 (m-90) cc_final: 0.5728 (m100) outliers start: 43 outliers final: 29 residues processed: 274 average time/residue: 0.1191 time to fit residues: 46.3134 Evaluate side-chains 275 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 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 D residue 544 THR 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 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 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 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 14 SER Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 545 GLU 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: 0.9990 chunk 21 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.141125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114144 restraints weight = 21504.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.111830 restraints weight = 51294.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112548 restraints weight = 46313.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112484 restraints weight = 30152.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.112841 restraints weight = 28740.845| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13821 Z= 0.188 Angle : 0.717 11.140 18834 Z= 0.341 Chirality : 0.048 0.265 2166 Planarity : 0.005 0.059 2337 Dihedral : 10.057 73.566 2667 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.64 % Favored : 97.11 % Rotamer: Outliers : 3.46 % Allowed : 12.70 % Favored : 83.84 % 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: -0.27 (0.21), residues: 1629 helix: 1.58 (0.39), residues: 174 sheet: -0.57 (0.20), residues: 687 loop : -0.04 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 587 TYR 0.022 0.002 TYR H 100 PHE 0.018 0.002 PHE J 72 TRP 0.041 0.002 TRP J 36 HIS 0.003 0.001 HIS D 549 Details of bonding type rmsd covalent geometry : bond 0.00436 (13764) covalent geometry : angle 0.67853 (18678) SS BOND : bond 0.00248 ( 15) SS BOND : angle 1.03044 ( 30) hydrogen bonds : bond 0.04080 ( 489) hydrogen bonds : angle 5.29335 ( 1251) link_ALPHA1-3 : bond 0.01594 ( 6) link_ALPHA1-3 : angle 1.25086 ( 18) link_ALPHA1-6 : bond 0.00964 ( 6) link_ALPHA1-6 : angle 2.01483 ( 18) link_BETA1-4 : bond 0.01522 ( 15) link_BETA1-4 : angle 3.40606 ( 45) link_NAG-ASN : bond 0.00534 ( 15) link_NAG-ASN : angle 3.12246 ( 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 294 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 0.487 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: 0.7068 (OUTLIER) cc_final: 0.6321 (m-10) REVERT: A 100 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: J 32 LYS cc_start: 0.8421 (pttt) cc_final: 0.8167 (mmtt) REVERT: D 510 LYS cc_start: 0.8603 (ptpt) cc_final: 0.7316 (mmtt) REVERT: D 551 GLN cc_start: 0.8122 (tp40) cc_final: 0.7467 (tp40) REVERT: D 565 THR cc_start: 0.8659 (p) cc_final: 0.8300 (t) REVERT: D 597 TRP cc_start: 0.6404 (m-90) cc_final: 0.5944 (m100) REVERT: B 130 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7232 (mtm-85) REVERT: B 261 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: K 86 VAL cc_start: 0.7210 (OUTLIER) cc_final: 0.6871 (p) REVERT: E 510 LYS cc_start: 0.8692 (ptpt) cc_final: 0.7360 (mmtt) REVERT: E 565 THR cc_start: 0.8717 (p) cc_final: 0.8431 (t) REVERT: E 597 TRP cc_start: 0.6339 (m-90) cc_final: 0.5921 (m100) REVERT: C 99 TYR cc_start: 0.6952 (OUTLIER) cc_final: 0.5828 (m-10) REVERT: C 184 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8931 (pp) REVERT: C 261 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: F 510 LYS cc_start: 0.8539 (ptpt) cc_final: 0.7176 (mmtt) REVERT: F 565 THR cc_start: 0.8779 (p) cc_final: 0.8355 (t) REVERT: F 578 GLU cc_start: 0.7595 (tt0) cc_final: 0.7352 (tt0) REVERT: F 597 TRP cc_start: 0.6320 (m-90) cc_final: 0.5838 (m100) outliers start: 48 outliers final: 34 residues processed: 270 average time/residue: 0.1261 time to fit residues: 48.5656 Evaluate side-chains 281 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 100 GLU 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 69 VAL 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 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 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 H residue 130 THR 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 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 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 545 GLU 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: 0.0170 chunk 154 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 chunk 21 optimal weight: 0.8980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 43 GLN B 39 HIS ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115763 restraints weight = 21531.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113998 restraints weight = 58543.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114614 restraints weight = 48933.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114340 restraints weight = 30907.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114720 restraints weight = 30184.690| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13821 Z= 0.147 Angle : 0.700 14.725 18834 Z= 0.332 Chirality : 0.047 0.259 2166 Planarity : 0.005 0.066 2337 Dihedral : 9.629 69.346 2667 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.58 % Favored : 97.18 % Rotamer: Outliers : 3.46 % Allowed : 13.56 % Favored : 82.97 % 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: -0.26 (0.21), residues: 1629 helix: 1.77 (0.39), residues: 174 sheet: -0.63 (0.20), residues: 669 loop : -0.02 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 587 TYR 0.029 0.002 TYR H 85 PHE 0.024 0.001 PHE E 592 TRP 0.063 0.003 TRP J 36 HIS 0.004 0.001 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00326 (13764) covalent geometry : angle 0.66645 (18678) SS BOND : bond 0.00180 ( 15) SS BOND : angle 1.02475 ( 30) hydrogen bonds : bond 0.03664 ( 489) hydrogen bonds : angle 5.21711 ( 1251) link_ALPHA1-3 : bond 0.01625 ( 6) link_ALPHA1-3 : angle 1.27386 ( 18) link_ALPHA1-6 : bond 0.01041 ( 6) link_ALPHA1-6 : angle 1.99194 ( 18) link_BETA1-4 : bond 0.01557 ( 15) link_BETA1-4 : angle 3.27610 ( 45) link_NAG-ASN : bond 0.00498 ( 15) link_NAG-ASN : angle 2.63353 ( 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 293 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 0.510 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 99 TYR cc_start: 0.6939 (OUTLIER) cc_final: 0.6179 (m-10) REVERT: A 100 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: A 231 GLU cc_start: 0.7189 (mp0) cc_final: 0.6973 (mp0) REVERT: J 32 LYS cc_start: 0.8387 (pttt) cc_final: 0.8182 (mmtt) REVERT: D 510 LYS cc_start: 0.8518 (ptpt) cc_final: 0.7239 (mmtt) REVERT: D 565 THR cc_start: 0.8564 (p) cc_final: 0.8263 (t) REVERT: D 597 TRP cc_start: 0.6446 (m-90) cc_final: 0.5993 (m100) REVERT: B 130 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7215 (mtm-85) REVERT: B 261 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: K 92 TYR cc_start: 0.5297 (OUTLIER) cc_final: 0.4772 (m-80) REVERT: E 510 LYS cc_start: 0.8637 (ptpt) cc_final: 0.7271 (mmtt) REVERT: E 565 THR cc_start: 0.8686 (p) cc_final: 0.8424 (t) REVERT: E 597 TRP cc_start: 0.6355 (m-90) cc_final: 0.5923 (m100) REVERT: C 184 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8869 (pp) REVERT: C 261 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: C 265 LYS cc_start: 0.8657 (mttt) cc_final: 0.8418 (mttt) REVERT: F 510 LYS cc_start: 0.8514 (ptpt) cc_final: 0.7134 (mmtt) REVERT: F 551 GLN cc_start: 0.8148 (tp40) cc_final: 0.7881 (tp40) REVERT: F 565 THR cc_start: 0.8761 (p) cc_final: 0.8382 (t) REVERT: F 578 GLU cc_start: 0.7570 (tt0) cc_final: 0.7332 (tt0) REVERT: F 597 TRP cc_start: 0.6427 (m-90) cc_final: 0.5900 (m100) outliers start: 48 outliers final: 33 residues processed: 274 average time/residue: 0.1326 time to fit residues: 51.2770 Evaluate side-chains 273 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 100 GLU 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 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 D residue 544 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR 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 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 H residue 121 ASP Chi-restraints excluded: chain H residue 130 THR 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 E residue 577 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 79 LEU 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: 1.9990 chunk 0 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 160 optimal weight: 0.5980 chunk 23 optimal weight: 30.0000 chunk 138 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 68 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN K 39 GLN C 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.140507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108718 restraints weight = 21506.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102125 restraints weight = 23503.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102274 restraints weight = 29921.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102808 restraints weight = 24743.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102841 restraints weight = 21830.171| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13821 Z= 0.175 Angle : 0.707 11.677 18834 Z= 0.335 Chirality : 0.047 0.262 2166 Planarity : 0.005 0.064 2337 Dihedral : 9.339 65.562 2667 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.89 % Favored : 96.81 % Rotamer: Outliers : 3.90 % Allowed : 13.42 % Favored : 82.68 % 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: -0.46 (0.21), residues: 1629 helix: 1.68 (0.39), residues: 174 sheet: -0.77 (0.19), residues: 678 loop : -0.16 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 57 TYR 0.020 0.002 TYR I 100 PHE 0.012 0.001 PHE J 72 TRP 0.032 0.002 TRP J 36 HIS 0.004 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00405 (13764) covalent geometry : angle 0.67545 (18678) SS BOND : bond 0.00239 ( 15) SS BOND : angle 0.92042 ( 30) hydrogen bonds : bond 0.03909 ( 489) hydrogen bonds : angle 5.17330 ( 1251) link_ALPHA1-3 : bond 0.01581 ( 6) link_ALPHA1-3 : angle 1.42123 ( 18) link_ALPHA1-6 : bond 0.00984 ( 6) link_ALPHA1-6 : angle 1.99380 ( 18) link_BETA1-4 : bond 0.01482 ( 15) link_BETA1-4 : angle 3.30924 ( 45) link_NAG-ASN : bond 0.00427 ( 15) link_NAG-ASN : angle 2.46349 ( 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 297 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 243 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6309 (m-10) REVERT: A 100 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: A 231 GLU cc_start: 0.7139 (mp0) cc_final: 0.6847 (mp0) REVERT: G 54 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6625 (tt) REVERT: J 32 LYS cc_start: 0.8892 (pttt) cc_final: 0.8267 (mmtt) REVERT: D 510 LYS cc_start: 0.8641 (ptpt) cc_final: 0.7274 (mmtt) REVERT: D 565 THR cc_start: 0.8626 (p) cc_final: 0.8267 (t) REVERT: D 597 TRP cc_start: 0.6414 (m-90) cc_final: 0.5982 (m100) REVERT: B 130 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7186 (mtm-85) REVERT: B 261 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.8222 (m-80) REVERT: K 91 GLN cc_start: 0.6492 (pp30) cc_final: 0.5758 (pp30) REVERT: K 92 TYR cc_start: 0.5673 (OUTLIER) cc_final: 0.4973 (m-80) REVERT: E 510 LYS cc_start: 0.8679 (ptpt) cc_final: 0.7291 (mmtt) REVERT: E 565 THR cc_start: 0.8703 (p) cc_final: 0.8417 (t) REVERT: E 597 TRP cc_start: 0.6378 (m-90) cc_final: 0.5949 (m100) REVERT: C 99 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6035 (m-10) REVERT: C 184 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8912 (pp) REVERT: C 261 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.8292 (m-80) REVERT: C 265 LYS cc_start: 0.8693 (mttt) cc_final: 0.8449 (mttt) REVERT: I 57 ARG cc_start: 0.7189 (mtp180) cc_final: 0.6972 (ttt180) REVERT: F 510 LYS cc_start: 0.8550 (ptpt) cc_final: 0.7169 (mmtt) REVERT: F 565 THR cc_start: 0.8720 (p) cc_final: 0.8343 (t) REVERT: F 578 GLU cc_start: 0.7463 (tt0) cc_final: 0.7225 (tt0) REVERT: F 597 TRP cc_start: 0.6321 (m-90) cc_final: 0.5832 (m100) outliers start: 54 outliers final: 37 residues processed: 276 average time/residue: 0.1209 time to fit residues: 47.7322 Evaluate side-chains 280 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 100 GLU 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 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 J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR 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 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 H residue 130 THR 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 E residue 577 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 87 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.140888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.117450 restraints weight = 21240.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117296 restraints weight = 57570.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115780 restraints weight = 45884.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115074 restraints weight = 39048.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115446 restraints weight = 28139.908| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13821 Z= 0.160 Angle : 0.738 15.197 18834 Z= 0.348 Chirality : 0.048 0.360 2166 Planarity : 0.006 0.139 2337 Dihedral : 9.103 61.811 2667 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.52 % Favored : 97.11 % Rotamer: Outliers : 4.18 % Allowed : 14.14 % Favored : 81.67 % 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: -0.47 (0.21), residues: 1629 helix: 1.78 (0.39), residues: 174 sheet: -0.78 (0.20), residues: 678 loop : -0.19 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 587 TYR 0.021 0.002 TYR G 85 PHE 0.013 0.001 PHE J 72 TRP 0.072 0.002 TRP L 36 HIS 0.004 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00365 (13764) covalent geometry : angle 0.69161 (18678) SS BOND : bond 0.00289 ( 15) SS BOND : angle 1.29527 ( 30) hydrogen bonds : bond 0.03786 ( 489) hydrogen bonds : angle 5.16875 ( 1251) link_ALPHA1-3 : bond 0.01597 ( 6) link_ALPHA1-3 : angle 1.45543 ( 18) link_ALPHA1-6 : bond 0.00992 ( 6) link_ALPHA1-6 : angle 1.97945 ( 18) link_BETA1-4 : bond 0.01514 ( 15) link_BETA1-4 : angle 3.27646 ( 45) link_NAG-ASN : bond 0.00418 ( 15) link_NAG-ASN : angle 3.89484 ( 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 306 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 248 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.6210 (m-10) REVERT: A 100 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: A 231 GLU cc_start: 0.7201 (mp0) cc_final: 0.6890 (mp0) REVERT: G 33 LYS cc_start: 0.5788 (OUTLIER) cc_final: 0.4889 (mttm) REVERT: G 54 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6654 (tt) REVERT: D 510 LYS cc_start: 0.8579 (ptpt) cc_final: 0.7272 (mmtt) REVERT: D 565 THR cc_start: 0.8685 (p) cc_final: 0.8334 (t) REVERT: D 597 TRP cc_start: 0.6463 (m-90) cc_final: 0.6024 (m100) REVERT: B 130 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7205 (mtm-85) REVERT: K 91 GLN cc_start: 0.5550 (pp30) cc_final: 0.5295 (pp30) REVERT: K 92 TYR cc_start: 0.5407 (OUTLIER) cc_final: 0.4713 (m-80) REVERT: E 510 LYS cc_start: 0.8661 (ptpt) cc_final: 0.7299 (mmtt) REVERT: E 551 GLN cc_start: 0.8371 (tp40) cc_final: 0.7944 (tp40) REVERT: E 565 THR cc_start: 0.8801 (p) cc_final: 0.8503 (t) REVERT: E 597 TRP cc_start: 0.6377 (m-90) cc_final: 0.6028 (m100) REVERT: C 99 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.6041 (m-10) REVERT: C 184 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8869 (pp) REVERT: C 223 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8427 (p) REVERT: I 54 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6838 (tt) REVERT: I 121 ASP cc_start: 0.6969 (t70) cc_final: 0.6533 (t70) REVERT: F 510 LYS cc_start: 0.8528 (ptpt) cc_final: 0.7166 (mmtt) REVERT: F 565 THR cc_start: 0.8777 (p) cc_final: 0.8360 (t) REVERT: F 578 GLU cc_start: 0.7457 (tt0) cc_final: 0.7232 (tt0) REVERT: F 597 TRP cc_start: 0.6370 (m-90) cc_final: 0.5884 (m100) outliers start: 58 outliers final: 38 residues processed: 286 average time/residue: 0.1288 time to fit residues: 52.2585 Evaluate side-chains 285 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 237 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 100 GLU 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 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 J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain B residue 82 VAL 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 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 H residue 130 THR 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 E residue 577 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 TYR 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 54 ILE 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 L residue 47 LEU Chi-restraints excluded: chain L residue 48 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 86 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 93 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 136 optimal weight: 0.0470 chunk 115 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 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 = 0.3757 r_free = 0.3757 target = 0.142057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119494 restraints weight = 21558.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119197 restraints weight = 57604.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117494 restraints weight = 47243.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116771 restraints weight = 43442.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116997 restraints weight = 29751.711| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13821 Z= 0.137 Angle : 0.707 12.284 18834 Z= 0.337 Chirality : 0.046 0.257 2166 Planarity : 0.005 0.070 2337 Dihedral : 8.689 59.371 2667 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.89 % Favored : 96.75 % Rotamer: Outliers : 3.17 % Allowed : 15.30 % Favored : 81.53 % 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: -0.41 (0.21), residues: 1629 helix: 1.81 (0.39), residues: 177 sheet: -0.72 (0.20), residues: 657 loop : -0.20 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 587 TYR 0.021 0.002 TYR L 50 PHE 0.020 0.001 PHE J 72 TRP 0.083 0.003 TRP J 36 HIS 0.004 0.001 HIS F 549 Details of bonding type rmsd covalent geometry : bond 0.00302 (13764) covalent geometry : angle 0.66828 (18678) SS BOND : bond 0.00271 ( 15) SS BOND : angle 1.54291 ( 30) hydrogen bonds : bond 0.03651 ( 489) hydrogen bonds : angle 5.12084 ( 1251) link_ALPHA1-3 : bond 0.01661 ( 6) link_ALPHA1-3 : angle 1.52650 ( 18) link_ALPHA1-6 : bond 0.01065 ( 6) link_ALPHA1-6 : angle 1.88976 ( 18) link_BETA1-4 : bond 0.01514 ( 15) link_BETA1-4 : angle 3.20458 ( 45) link_NAG-ASN : bond 0.00369 ( 15) link_NAG-ASN : angle 3.07440 ( 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 288 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: A 231 GLU cc_start: 0.7203 (mp0) cc_final: 0.6896 (mp0) REVERT: G 33 LYS cc_start: 0.5781 (OUTLIER) cc_final: 0.4888 (mttm) REVERT: G 54 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.6841 (tt) REVERT: J 32 LYS cc_start: 0.7690 (mmtt) cc_final: 0.7476 (mmtt) REVERT: D 510 LYS cc_start: 0.8542 (ptpt) cc_final: 0.7236 (mmtt) REVERT: D 565 THR cc_start: 0.8628 (p) cc_final: 0.8310 (t) REVERT: D 597 TRP cc_start: 0.6404 (m-90) cc_final: 0.5983 (m100) REVERT: B 130 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7205 (mtm-85) REVERT: K 92 TYR cc_start: 0.5413 (OUTLIER) cc_final: 0.5068 (m-80) REVERT: E 510 LYS cc_start: 0.8646 (ptpt) cc_final: 0.7313 (mmtt) REVERT: E 551 GLN cc_start: 0.8371 (tp40) cc_final: 0.7936 (tp40) REVERT: E 565 THR cc_start: 0.8858 (p) cc_final: 0.8551 (t) REVERT: E 597 TRP cc_start: 0.6349 (m-90) cc_final: 0.5934 (m100) REVERT: C 99 TYR cc_start: 0.6963 (OUTLIER) cc_final: 0.6217 (m-10) REVERT: C 184 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8863 (pp) REVERT: I 54 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6849 (tt) REVERT: I 121 ASP cc_start: 0.6976 (t70) cc_final: 0.6588 (t70) REVERT: F 510 LYS cc_start: 0.8480 (ptpt) cc_final: 0.7115 (mmtt) REVERT: F 565 THR cc_start: 0.8817 (p) cc_final: 0.8430 (t) REVERT: F 578 GLU cc_start: 0.7493 (tt0) cc_final: 0.7283 (tt0) REVERT: F 597 TRP cc_start: 0.6333 (m-90) cc_final: 0.5860 (m100) outliers start: 44 outliers final: 30 residues processed: 276 average time/residue: 0.1272 time to fit residues: 50.0517 Evaluate side-chains 267 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 239 LEU 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 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 D residue 577 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain H residue 130 THR 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 577 THR Chi-restraints excluded: chain C residue 96 VAL 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 I residue 5 VAL Chi-restraints excluded: chain I residue 54 ILE 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 47 LEU Chi-restraints excluded: chain L residue 48 LEU 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 89 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.140753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.116931 restraints weight = 21407.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115969 restraints weight = 58635.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116014 restraints weight = 51071.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115276 restraints weight = 34466.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115600 restraints weight = 30085.950| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.5090 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= 0.169 Angle : 0.725 11.992 18834 Z= 0.346 Chirality : 0.047 0.241 2166 Planarity : 0.005 0.066 2337 Dihedral : 8.493 59.561 2667 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.07 % Favored : 96.62 % Rotamer: Outliers : 3.17 % Allowed : 15.22 % Favored : 81.60 % 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: 1.72 (0.39), residues: 177 sheet: -0.73 (0.20), residues: 657 loop : -0.28 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 587 TYR 0.017 0.002 TYR I 100 PHE 0.018 0.001 PHE J 72 TRP 0.063 0.002 TRP J 36 HIS 0.004 0.001 HIS F 549 Details of bonding type rmsd covalent geometry : bond 0.00391 (13764) covalent geometry : angle 0.69064 (18678) SS BOND : bond 0.00310 ( 15) SS BOND : angle 1.34686 ( 30) hydrogen bonds : bond 0.03939 ( 489) hydrogen bonds : angle 5.06936 ( 1251) link_ALPHA1-3 : bond 0.01598 ( 6) link_ALPHA1-3 : angle 1.65164 ( 18) link_ALPHA1-6 : bond 0.00918 ( 6) link_ALPHA1-6 : angle 1.73764 ( 18) link_BETA1-4 : bond 0.01488 ( 15) link_BETA1-4 : angle 3.35118 ( 45) link_NAG-ASN : bond 0.00358 ( 15) link_NAG-ASN : angle 2.75234 ( 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 281 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6291 (m-10) REVERT: A 100 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: A 231 GLU cc_start: 0.7201 (mp0) cc_final: 0.6918 (mp0) REVERT: G 33 LYS cc_start: 0.5798 (OUTLIER) cc_final: 0.4902 (mttm) REVERT: G 54 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6940 (tt) REVERT: G 84 LEU cc_start: 0.6005 (pp) cc_final: 0.5791 (pt) REVERT: J 32 LYS cc_start: 0.7647 (mmtt) cc_final: 0.7432 (mmtt) REVERT: D 510 LYS cc_start: 0.8582 (ptpt) cc_final: 0.7233 (mmtt) REVERT: D 565 THR cc_start: 0.8631 (p) cc_final: 0.8290 (t) REVERT: D 597 TRP cc_start: 0.6479 (m-90) cc_final: 0.6052 (m100) REVERT: B 130 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7266 (mtm-85) REVERT: K 92 TYR cc_start: 0.5459 (OUTLIER) cc_final: 0.5146 (m-80) REVERT: E 510 LYS cc_start: 0.8673 (ptpt) cc_final: 0.7339 (mmtt) REVERT: E 551 GLN cc_start: 0.8374 (tp40) cc_final: 0.7981 (tp40) REVERT: E 565 THR cc_start: 0.8797 (p) cc_final: 0.8508 (t) REVERT: E 597 TRP cc_start: 0.6377 (m-90) cc_final: 0.6024 (m100) REVERT: C 99 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.5914 (m-10) REVERT: C 184 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8884 (pp) REVERT: I 54 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.6974 (tt) REVERT: I 121 ASP cc_start: 0.6917 (t70) cc_final: 0.6554 (t70) REVERT: F 510 LYS cc_start: 0.8510 (ptpt) cc_final: 0.7139 (mmtt) REVERT: F 565 THR cc_start: 0.8801 (p) cc_final: 0.8381 (t) REVERT: F 578 GLU cc_start: 0.7478 (tt0) cc_final: 0.7240 (tt0) REVERT: F 597 TRP cc_start: 0.6367 (m-90) cc_final: 0.5904 (m100) outliers start: 44 outliers final: 33 residues processed: 270 average time/residue: 0.1304 time to fit residues: 50.1283 Evaluate side-chains 275 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 54 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 D residue 577 THR 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 130 THR 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 E residue 577 THR Chi-restraints excluded: chain C residue 96 VAL 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 I residue 5 VAL Chi-restraints excluded: chain I residue 54 ILE 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 47 LEU Chi-restraints excluded: chain L residue 48 LEU 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 31 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 161 optimal weight: 0.5980 chunk 155 optimal weight: 0.0050 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.142591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116688 restraints weight = 21473.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.115010 restraints weight = 56670.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115587 restraints weight = 51084.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115633 restraints weight = 32514.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115944 restraints weight = 31588.060| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13821 Z= 0.125 Angle : 0.681 10.335 18834 Z= 0.326 Chirality : 0.045 0.228 2166 Planarity : 0.005 0.069 2337 Dihedral : 7.411 59.865 2667 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.52 % Favored : 97.18 % Rotamer: Outliers : 2.74 % Allowed : 15.80 % Favored : 81.46 % 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: -0.37 (0.21), residues: 1629 helix: 1.93 (0.39), residues: 177 sheet: -0.66 (0.20), residues: 657 loop : -0.23 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 587 TYR 0.022 0.001 TYR L 50 PHE 0.018 0.001 PHE J 72 TRP 0.062 0.002 TRP J 36 HIS 0.004 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00272 (13764) covalent geometry : angle 0.64758 (18678) SS BOND : bond 0.00214 ( 15) SS BOND : angle 1.31729 ( 30) hydrogen bonds : bond 0.03319 ( 489) hydrogen bonds : angle 5.00552 ( 1251) link_ALPHA1-3 : bond 0.01635 ( 6) link_ALPHA1-3 : angle 1.79895 ( 18) link_ALPHA1-6 : bond 0.00873 ( 6) link_ALPHA1-6 : angle 1.72452 ( 18) link_BETA1-4 : bond 0.01509 ( 15) link_BETA1-4 : angle 3.29987 ( 45) link_NAG-ASN : bond 0.00334 ( 15) link_NAG-ASN : angle 2.35078 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2028.55 seconds wall clock time: 36 minutes 3.65 seconds (2163.65 seconds total)