Starting phenix.real_space_refine on Thu Sep 26 17:07:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfb_22848/09_2024/7kfb_22848.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfb_22848/09_2024/7kfb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfb_22848/09_2024/7kfb_22848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfb_22848/09_2024/7kfb_22848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfb_22848/09_2024/7kfb_22848.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfb_22848/09_2024/7kfb_22848.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 7.10, per 1000 atoms: 0.53 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=5, 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 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: 3.99 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 2.08 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: 4.57 Time building geometry restraints manager: 4.51 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: 8312 21.39 - 42.78: 169 42.78 - 64.16: 48 64.16 - 85.55: 45 85.55 - 106.94: 24 Dihedral angle restraints: 8598 sinusoidal: 3888 harmonic: 4710 Sorted by residual: 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=" C TYR C 99 " pdb=" N TYR C 99 " pdb=" CA TYR C 99 " pdb=" CB TYR C 99 " ideal model delta harmonic sigma weight residual -122.60 -108.64 -13.96 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" C TYR B 99 " pdb=" N TYR B 99 " pdb=" CA TYR B 99 " pdb=" CB TYR B 99 " ideal model delta harmonic sigma weight residual -122.60 -108.64 -13.96 0 2.50e+00 1.60e-01 3.12e+01 ... (remaining 8595 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: 2.02 - 2.59: 99 2.59 - 3.17: 11030 3.17 - 3.75: 19992 3.75 - 4.32: 30411 4.32 - 4.90: 48399 Nonbonded interactions: 109931 Sorted by model distance: nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS K 23 " pdb=" SG CYS K 89 " model vdw 2.018 3.760 nonbonded pdb=" SG CYS B 121 " pdb=" SG CYS B 147 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS C 121 " pdb=" SG CYS C 147 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 101 " model vdw 2.022 3.760 ... (remaining 109926 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: 0.00 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 31.780 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.220 ------------------------------------------------------------------------------- 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 13764 Z= 1.432 Angle : 1.851 11.314 18678 Z= 1.210 Chirality : 0.125 0.525 2166 Planarity : 0.009 0.060 2337 Dihedral : 13.131 106.938 5601 Min Nonbonded Distance : 2.017 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (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 TRP 0.035 0.009 TRP L 36 HIS 0.007 0.003 HIS E 516 PHE 0.019 0.005 PHE H 122 TYR 0.105 0.012 TYR B 99 ARG 0.012 0.001 ARG H 77 *********************** 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 fitting. rotamer outliers: 3 poor density : 402 time to evaluate : 1.590 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 99 TYR cc_start: 0.7462 (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: 0.6232 (tp40) cc_final: 0.5623 (mp10) REVERT: G 130 THR cc_start: 0.6451 (t) cc_final: 0.6233 (m) REVERT: J 32 LYS cc_start: 0.8102 (pttt) cc_final: 0.7770 (mmmt) REVERT: J 59 ILE cc_start: 0.2137 (mm) cc_final: 0.1924 (mm) REVERT: J 61 ASP cc_start: 0.6874 (p0) cc_final: 0.6330 (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: 0.8654 (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: 0.7639 (mt0) REVERT: B 99 TYR cc_start: 0.7441 (m-10) cc_final: 0.6525 (m-10) REVERT: B 103 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8288 (mt-10) REVERT: B 114 LYS cc_start: 0.8072 (mttm) cc_final: 0.7819 (mttm) REVERT: H 39 TRP cc_start: 0.7228 (m100) cc_final: 0.6304 (m100) REVERT: H 87 GLN cc_start: 0.5715 (tp40) cc_final: 0.5339 (mp10) REVERT: K 61 ASP cc_start: 0.6962 (p0) cc_final: 0.6465 (t70) REVERT: E 510 LYS cc_start: 0.8676 (ptpt) cc_final: 0.7689 (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: 0.5680 (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: 0.6150 (m100) REVERT: I 87 GLN cc_start: 0.5745 (tp40) cc_final: 0.5449 (mp10) REVERT: L 32 LYS cc_start: 0.8039 (pttt) cc_final: 0.7784 (ptmm) REVERT: L 33 TYR cc_start: 0.6644 (m-80) cc_final: 0.6411 (m-80) REVERT: L 61 ASP cc_start: 0.6634 (p0) cc_final: 0.6203 (t0) REVERT: L 73 THR cc_start: 0.7689 (m) cc_final: 0.7470 (t) REVERT: L 97 TRP cc_start: 0.6024 (m-10) cc_final: 0.5696 (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: 0.5423 (m100) outliers start: 3 outliers final: 0 residues processed: 402 average time/residue: 0.3089 time to fit residues: 168.1942 Evaluate side-chains 260 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13764 Z= 0.301 Angle : 0.758 7.267 18678 Z= 0.388 Chirality : 0.050 0.247 2166 Planarity : 0.005 0.045 2337 Dihedral : 12.592 90.072 2667 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.09 % Favored : 97.73 % Rotamer: Outliers : 1.80 % Allowed : 9.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1629 helix: 2.64 (0.37), residues: 147 sheet: -0.46 (0.19), residues: 705 loop : 0.53 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 36 HIS 0.004 0.001 HIS E 549 PHE 0.041 0.002 PHE J 72 TYR 0.021 0.002 TYR H 118 ARG 0.009 0.001 ARG F 587 *********************** 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 fitting. rotamer outliers: 25 poor density : 279 time to evaluate : 1.391 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: 0.7775 (mt-10) cc_final: 0.7368 (mp0) REVERT: G 39 TRP cc_start: 0.7014 (m100) cc_final: 0.6350 (m100) REVERT: G 87 GLN cc_start: 0.5870 (tp40) cc_final: 0.5300 (mp10) REVERT: J 36 TRP cc_start: 0.5785 (m100) cc_final: 0.5539 (m-10) REVERT: J 61 ASP cc_start: 0.7030 (p0) cc_final: 0.6571 (t0) REVERT: J 79 LEU cc_start: 0.6633 (tp) cc_final: 0.5904 (tt) REVERT: J 80 GLU cc_start: 0.5325 (mm-30) cc_final: 0.4995 (tp30) REVERT: J 90 HIS cc_start: 0.6501 (t-90) cc_final: 0.5937 (t70) REVERT: D 510 LYS cc_start: 0.8646 (ptpt) cc_final: 0.7343 (mmtt) REVERT: D 565 THR cc_start: 0.8641 (p) cc_final: 0.8362 (t) REVERT: D 587 ARG cc_start: 0.8225 (ttm110) cc_final: 0.8015 (mtp-110) REVERT: D 597 TRP cc_start: 0.6302 (m-90) cc_final: 0.5738 (m100) REVERT: B 100 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7693 (mp0) REVERT: H 87 GLN cc_start: 0.5684 (tp40) cc_final: 0.5251 (mp10) REVERT: K 61 ASP cc_start: 0.7208 (p0) cc_final: 0.6826 (t70) REVERT: K 80 GLU cc_start: 0.4949 (mm-30) cc_final: 0.4642 (tp30) REVERT: E 510 LYS cc_start: 0.8856 (ptpt) cc_final: 0.7618 (mmtt) REVERT: E 565 THR cc_start: 0.8862 (p) cc_final: 0.8642 (t) REVERT: E 578 GLU cc_start: 0.7933 (tt0) cc_final: 0.7672 (tt0) REVERT: E 597 TRP cc_start: 0.6310 (m-90) cc_final: 0.5825 (m100) REVERT: C 100 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7338 (mp0) REVERT: I 87 GLN cc_start: 0.5477 (tp40) cc_final: 0.5154 (mp10) REVERT: L 61 ASP cc_start: 0.7145 (p0) cc_final: 0.6708 (t0) REVERT: L 73 THR cc_start: 0.8079 (m) cc_final: 0.7800 (t) REVERT: L 90 HIS cc_start: 0.6591 (t-90) cc_final: 0.6044 (t70) REVERT: F 510 LYS cc_start: 0.8844 (ptpt) cc_final: 0.7492 (mmtt) REVERT: F 565 THR cc_start: 0.8845 (p) cc_final: 0.8544 (t) REVERT: F 597 TRP cc_start: 0.6203 (m-90) cc_final: 0.5729 (m100) outliers start: 25 outliers final: 21 residues processed: 291 average time/residue: 0.3080 time to fit residues: 123.7464 Evaluate side-chains 264 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 243 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR 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 40 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 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 564 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.0070 chunk 122 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 131 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 HIS F 516 HIS F 595 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13764 Z= 0.226 Angle : 0.664 10.683 18678 Z= 0.332 Chirality : 0.046 0.240 2166 Planarity : 0.004 0.048 2337 Dihedral : 11.237 82.613 2667 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.97 % Rotamer: Outliers : 2.89 % Allowed : 11.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1629 helix: 2.56 (0.38), residues: 156 sheet: -0.35 (0.20), residues: 636 loop : 0.20 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 36 HIS 0.004 0.001 HIS L 90 PHE 0.022 0.002 PHE K 99 TYR 0.029 0.002 TYR K 92 ARG 0.008 0.001 ARG E 587 *********************** 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 309 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 269 time to evaluate : 1.466 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: 0.7652 (mt-10) cc_final: 0.7260 (mp0) REVERT: A 229 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8020 (pp20) REVERT: A 231 GLU cc_start: 0.8474 (mp0) cc_final: 0.8078 (mp0) REVERT: G 87 GLN cc_start: 0.5312 (tp40) cc_final: 0.4925 (mp10) REVERT: J 61 ASP cc_start: 0.7084 (p0) cc_final: 0.6539 (t0) REVERT: J 63 PHE cc_start: 0.5725 (m-80) cc_final: 0.5499 (m-80) REVERT: J 79 LEU cc_start: 0.6688 (tp) cc_final: 0.5997 (tt) REVERT: J 80 GLU cc_start: 0.5384 (mm-30) cc_final: 0.5082 (tp30) REVERT: J 90 HIS cc_start: 0.6838 (t-90) cc_final: 0.6299 (t70) REVERT: D 510 LYS cc_start: 0.8621 (ptpt) cc_final: 0.7282 (mmtt) REVERT: D 565 THR cc_start: 0.8766 (p) cc_final: 0.8484 (t) REVERT: D 587 ARG cc_start: 0.8364 (ttm110) cc_final: 0.7993 (mtp-110) REVERT: D 597 TRP cc_start: 0.6228 (m-90) cc_final: 0.5785 (m100) REVERT: B 100 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7578 (mp0) REVERT: B 130 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8032 (mtm-85) REVERT: H 33 LYS cc_start: 0.5579 (OUTLIER) cc_final: 0.4907 (mttm) REVERT: H 87 GLN cc_start: 0.5756 (tp40) cc_final: 0.4977 (pm20) REVERT: H 100 TYR cc_start: 0.5257 (m-80) cc_final: 0.5049 (m-80) REVERT: K 32 LYS cc_start: 0.7728 (ptmm) cc_final: 0.7473 (mmtt) REVERT: K 61 ASP cc_start: 0.7253 (p0) cc_final: 0.6915 (t70) REVERT: K 80 GLU cc_start: 0.4990 (mm-30) cc_final: 0.4716 (tp30) REVERT: K 92 TYR cc_start: 0.5107 (OUTLIER) cc_final: 0.4248 (m-80) REVERT: K 97 TRP cc_start: 0.5574 (m-90) cc_final: 0.5109 (m-10) REVERT: E 510 LYS cc_start: 0.8855 (ptpt) cc_final: 0.7631 (mmtt) REVERT: E 597 TRP cc_start: 0.6239 (m-90) cc_final: 0.5694 (m100) REVERT: C 100 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7252 (mp0) REVERT: C 184 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8956 (pp) REVERT: C 231 GLU cc_start: 0.8312 (mp0) cc_final: 0.7815 (mp0) REVERT: C 261 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: I 87 GLN cc_start: 0.5542 (tp40) cc_final: 0.5094 (mp10) REVERT: I 99 TYR cc_start: 0.6647 (m-80) cc_final: 0.6364 (m-10) REVERT: I 123 ILE cc_start: 0.7438 (mp) cc_final: 0.7236 (mp) REVERT: L 59 ILE cc_start: 0.2376 (OUTLIER) cc_final: 0.2064 (pt) REVERT: L 61 ASP cc_start: 0.7271 (p0) cc_final: 0.6874 (t0) REVERT: L 90 HIS cc_start: 0.6797 (t-90) cc_final: 0.6070 (t70) REVERT: F 510 LYS cc_start: 0.8835 (ptpt) cc_final: 0.7486 (mmtt) REVERT: F 551 GLN cc_start: 0.8527 (tp40) cc_final: 0.8107 (tp40) REVERT: F 565 THR cc_start: 0.8896 (p) cc_final: 0.8570 (t) REVERT: F 578 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7696 (tt0) REVERT: F 597 TRP cc_start: 0.6130 (m-90) cc_final: 0.5602 (m100) outliers start: 40 outliers final: 21 residues processed: 294 average time/residue: 0.2901 time to fit residues: 118.8942 Evaluate side-chains 267 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU 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 B residue 65 SER 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 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 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 92 TYR 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 59 ILE 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 145 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 98 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 140 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 13764 Z= 0.456 Angle : 0.771 13.179 18678 Z= 0.379 Chirality : 0.051 0.281 2166 Planarity : 0.005 0.049 2337 Dihedral : 10.830 79.690 2667 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.70 % Favored : 97.11 % Rotamer: Outliers : 4.40 % Allowed : 11.90 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1629 helix: 1.34 (0.40), residues: 174 sheet: -0.88 (0.19), residues: 702 loop : 0.03 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP L 36 HIS 0.005 0.002 HIS D 549 PHE 0.018 0.002 PHE L 72 TYR 0.026 0.003 TYR G 100 ARG 0.009 0.001 ARG E 587 *********************** 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 308 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 247 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6711 (m-10) REVERT: A 100 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: A 184 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8953 (pp) REVERT: A 227 THR cc_start: 0.7966 (t) cc_final: 0.7747 (p) REVERT: A 229 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7998 (pp20) REVERT: A 231 GLU cc_start: 0.8585 (mp0) cc_final: 0.8076 (mp0) REVERT: G 87 GLN cc_start: 0.5640 (tp40) cc_final: 0.4910 (pm20) REVERT: J 32 LYS cc_start: 0.8339 (pttt) cc_final: 0.7993 (mmtt) REVERT: J 61 ASP cc_start: 0.6886 (p0) cc_final: 0.6416 (t0) REVERT: J 79 LEU cc_start: 0.6645 (tp) cc_final: 0.5761 (tt) REVERT: J 80 GLU cc_start: 0.5458 (mm-30) cc_final: 0.5088 (tp30) REVERT: J 90 HIS cc_start: 0.6812 (t-90) cc_final: 0.6191 (t70) REVERT: D 510 LYS cc_start: 0.8857 (ptpt) cc_final: 0.7348 (mmtt) REVERT: D 565 THR cc_start: 0.8641 (p) cc_final: 0.8331 (t) REVERT: D 587 ARG cc_start: 0.8421 (ttm110) cc_final: 0.8082 (mtp-110) REVERT: D 597 TRP cc_start: 0.6516 (m-90) cc_final: 0.6071 (m100) REVERT: B 44 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7552 (mt0) REVERT: B 184 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8910 (pp) REVERT: B 261 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: H 87 GLN cc_start: 0.5722 (tp40) cc_final: 0.4845 (pm20) REVERT: H 99 TYR cc_start: 0.6757 (m-80) cc_final: 0.6519 (m-80) REVERT: H 100 TYR cc_start: 0.5192 (m-80) cc_final: 0.4973 (m-80) REVERT: K 32 LYS cc_start: 0.7897 (ptmm) cc_final: 0.7596 (mmtt) REVERT: K 61 ASP cc_start: 0.7145 (p0) cc_final: 0.6799 (t0) REVERT: K 80 GLU cc_start: 0.5037 (mm-30) cc_final: 0.4764 (tp30) REVERT: K 92 TYR cc_start: 0.5342 (OUTLIER) cc_final: 0.4449 (m-80) REVERT: K 97 TRP cc_start: 0.5765 (m-90) cc_final: 0.5092 (m-90) REVERT: E 510 LYS cc_start: 0.8901 (ptpt) cc_final: 0.7516 (mmtt) REVERT: E 551 GLN cc_start: 0.8596 (tp40) cc_final: 0.7995 (tp40) REVERT: E 597 TRP cc_start: 0.6431 (m-90) cc_final: 0.5929 (m100) REVERT: C 99 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.5684 (m-10) REVERT: C 100 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7625 (mp0) REVERT: C 231 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: C 261 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8009 (m-80) REVERT: I 87 GLN cc_start: 0.5689 (tp40) cc_final: 0.4874 (pm20) REVERT: I 99 TYR cc_start: 0.6527 (m-80) cc_final: 0.6117 (m-10) REVERT: L 61 ASP cc_start: 0.7203 (p0) cc_final: 0.6798 (t0) REVERT: L 90 HIS cc_start: 0.6808 (t-90) cc_final: 0.6114 (t70) REVERT: F 510 LYS cc_start: 0.8811 (ptpt) cc_final: 0.7340 (mmtt) REVERT: F 551 GLN cc_start: 0.8389 (tp40) cc_final: 0.7866 (tp40) REVERT: F 565 THR cc_start: 0.8945 (p) cc_final: 0.8528 (t) REVERT: F 597 TRP cc_start: 0.6398 (m-90) cc_final: 0.5841 (m100) outliers start: 61 outliers final: 37 residues processed: 285 average time/residue: 0.2691 time to fit residues: 108.6779 Evaluate side-chains 286 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 240 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 184 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 93 THR 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 L residue 92 TYR 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 130 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 133 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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** C 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13764 Z= 0.355 Angle : 0.693 9.988 18678 Z= 0.341 Chirality : 0.048 0.269 2166 Planarity : 0.005 0.053 2337 Dihedral : 10.383 75.532 2667 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.64 % Favored : 97.05 % Rotamer: Outliers : 4.47 % Allowed : 12.63 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.21), residues: 1629 helix: 1.48 (0.41), residues: 174 sheet: -0.87 (0.19), residues: 687 loop : -0.10 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 36 HIS 0.004 0.001 HIS F 549 PHE 0.015 0.002 PHE K 72 TYR 0.021 0.002 TYR K 92 ARG 0.012 0.001 ARG F 587 *********************** 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 308 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 246 time to evaluate : 1.591 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: 0.7350 (OUTLIER) cc_final: 0.6594 (m-10) REVERT: A 100 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: A 184 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8922 (pp) REVERT: A 231 GLU cc_start: 0.8562 (mp0) cc_final: 0.8034 (mp0) REVERT: G 33 LYS cc_start: 0.5351 (OUTLIER) cc_final: 0.4389 (mttm) REVERT: G 39 TRP cc_start: 0.6609 (m100) cc_final: 0.6315 (m100) REVERT: G 87 GLN cc_start: 0.5724 (tp40) cc_final: 0.4989 (pm20) REVERT: J 32 LYS cc_start: 0.8368 (pttt) cc_final: 0.7983 (mmtt) REVERT: J 61 ASP cc_start: 0.7057 (p0) cc_final: 0.6677 (t0) REVERT: J 79 LEU cc_start: 0.6684 (tp) cc_final: 0.5907 (tt) REVERT: J 80 GLU cc_start: 0.5495 (mm-30) cc_final: 0.5152 (tp30) REVERT: D 510 LYS cc_start: 0.8819 (ptpt) cc_final: 0.7246 (mmtt) REVERT: D 565 THR cc_start: 0.8702 (p) cc_final: 0.8440 (t) REVERT: D 587 ARG cc_start: 0.8413 (ttm110) cc_final: 0.8074 (mtp-110) REVERT: D 597 TRP cc_start: 0.6491 (m-90) cc_final: 0.6014 (m100) REVERT: B 99 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6831 (m-80) REVERT: B 100 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7677 (mp0) REVERT: B 184 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8818 (pp) REVERT: B 261 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: H 87 GLN cc_start: 0.5626 (tp40) cc_final: 0.4868 (pm20) REVERT: H 99 TYR cc_start: 0.6643 (m-80) cc_final: 0.6343 (m-80) REVERT: H 100 TYR cc_start: 0.5328 (m-80) cc_final: 0.5107 (m-80) REVERT: K 32 LYS cc_start: 0.8026 (ptmm) cc_final: 0.7669 (mmtt) REVERT: K 61 ASP cc_start: 0.7138 (p0) cc_final: 0.6765 (t0) REVERT: K 80 GLU cc_start: 0.4968 (mm-30) cc_final: 0.4611 (tp30) REVERT: K 92 TYR cc_start: 0.5131 (OUTLIER) cc_final: 0.4378 (m-80) REVERT: E 510 LYS cc_start: 0.8900 (ptpt) cc_final: 0.7510 (mmtt) REVERT: E 551 GLN cc_start: 0.8606 (tp40) cc_final: 0.8009 (tp40) REVERT: E 597 TRP cc_start: 0.6411 (m-90) cc_final: 0.5897 (m100) REVERT: C 99 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.5868 (m-10) REVERT: C 100 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7372 (mp0) REVERT: C 231 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: C 261 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: I 87 GLN cc_start: 0.5743 (tp40) cc_final: 0.5038 (pm20) REVERT: I 99 TYR cc_start: 0.6683 (m-80) cc_final: 0.6403 (m-10) REVERT: L 61 ASP cc_start: 0.7153 (p0) cc_final: 0.6761 (t0) REVERT: L 90 HIS cc_start: 0.6771 (t-90) cc_final: 0.6049 (t-170) REVERT: F 510 LYS cc_start: 0.8818 (ptpt) cc_final: 0.7349 (mmtt) REVERT: F 551 GLN cc_start: 0.8415 (tp40) cc_final: 0.8078 (tp40) REVERT: F 565 THR cc_start: 0.8953 (p) cc_final: 0.8542 (t) REVERT: F 578 GLU cc_start: 0.7988 (tt0) cc_final: 0.7753 (tt0) REVERT: F 587 ARG cc_start: 0.8403 (ttm110) cc_final: 0.8129 (mtp-110) REVERT: F 597 TRP cc_start: 0.6360 (m-90) cc_final: 0.5805 (m100) outliers start: 62 outliers final: 42 residues processed: 288 average time/residue: 0.2719 time to fit residues: 110.5868 Evaluate side-chains 292 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 239 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 184 LEU 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 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain B residue 65 SER 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 B residue 184 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 76 ILE 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 65 SER 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 C residue 231 GLU 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 93 THR Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 92 TYR 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 52 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** J 43 GLN H 42 GLN K 39 GLN C 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13764 Z= 0.244 Angle : 0.644 9.513 18678 Z= 0.315 Chirality : 0.047 0.262 2166 Planarity : 0.004 0.055 2337 Dihedral : 9.858 70.480 2667 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.70 % Favored : 96.93 % Rotamer: Outliers : 4.18 % Allowed : 13.71 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1629 helix: 1.72 (0.40), residues: 174 sheet: -0.87 (0.19), residues: 687 loop : -0.10 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 97 HIS 0.003 0.001 HIS F 549 PHE 0.015 0.001 PHE I 30 TYR 0.017 0.002 TYR G 100 ARG 0.012 0.001 ARG E 587 *********************** 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 317 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 259 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.6196 (m-10) REVERT: A 100 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: A 184 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8856 (pp) REVERT: A 231 GLU cc_start: 0.8603 (mp0) cc_final: 0.8054 (mp0) REVERT: G 33 LYS cc_start: 0.5231 (OUTLIER) cc_final: 0.4306 (mttm) REVERT: J 32 LYS cc_start: 0.8397 (pttt) cc_final: 0.8021 (mmtt) REVERT: J 61 ASP cc_start: 0.7066 (p0) cc_final: 0.6704 (t0) REVERT: J 79 LEU cc_start: 0.6699 (tp) cc_final: 0.5952 (tt) REVERT: J 80 GLU cc_start: 0.5445 (mm-30) cc_final: 0.5121 (tp30) REVERT: D 510 LYS cc_start: 0.8782 (ptpt) cc_final: 0.7261 (mmtt) REVERT: D 565 THR cc_start: 0.8734 (p) cc_final: 0.8479 (t) REVERT: D 587 ARG cc_start: 0.8415 (ttm110) cc_final: 0.8091 (mtp-110) REVERT: D 597 TRP cc_start: 0.6509 (m-90) cc_final: 0.6008 (m100) REVERT: B 61 ASN cc_start: 0.8496 (t0) cc_final: 0.8288 (m-40) REVERT: B 100 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7654 (mp0) REVERT: B 130 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7789 (mtm-85) REVERT: B 261 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: H 33 LYS cc_start: 0.5336 (OUTLIER) cc_final: 0.4531 (mttm) REVERT: H 87 GLN cc_start: 0.5631 (tp40) cc_final: 0.4874 (pm20) REVERT: H 99 TYR cc_start: 0.6673 (m-80) cc_final: 0.6472 (m-80) REVERT: H 100 TYR cc_start: 0.5428 (m-80) cc_final: 0.5199 (m-80) REVERT: K 32 LYS cc_start: 0.8030 (ptmm) cc_final: 0.7611 (mmtt) REVERT: K 61 ASP cc_start: 0.7163 (p0) cc_final: 0.6818 (t0) REVERT: K 80 GLU cc_start: 0.5012 (mm-30) cc_final: 0.4760 (tp30) REVERT: E 510 LYS cc_start: 0.8858 (ptpt) cc_final: 0.7413 (mmtt) REVERT: E 587 ARG cc_start: 0.8275 (ttm110) cc_final: 0.7947 (mtp-110) REVERT: E 597 TRP cc_start: 0.6375 (m-90) cc_final: 0.5869 (m100) REVERT: C 99 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.5875 (m-10) REVERT: C 100 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7276 (mp0) REVERT: C 231 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: C 261 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: I 19 ARG cc_start: 0.6147 (ttm170) cc_final: 0.5226 (ptm-80) REVERT: I 87 GLN cc_start: 0.5784 (tp40) cc_final: 0.5048 (mp10) REVERT: I 99 TYR cc_start: 0.6648 (m-80) cc_final: 0.6443 (m-10) REVERT: L 61 ASP cc_start: 0.7219 (p0) cc_final: 0.6821 (t0) REVERT: L 90 HIS cc_start: 0.6899 (t-90) cc_final: 0.5976 (t-170) REVERT: F 510 LYS cc_start: 0.8775 (ptpt) cc_final: 0.7319 (mmtt) REVERT: F 551 GLN cc_start: 0.8426 (tp40) cc_final: 0.8120 (tp40) REVERT: F 565 THR cc_start: 0.8954 (p) cc_final: 0.8573 (t) REVERT: F 578 GLU cc_start: 0.7923 (tt0) cc_final: 0.7698 (tt0) REVERT: F 587 ARG cc_start: 0.8388 (ttm110) cc_final: 0.8069 (mtp-110) REVERT: F 597 TRP cc_start: 0.6357 (m-90) cc_final: 0.5824 (m100) outliers start: 58 outliers final: 41 residues processed: 298 average time/residue: 0.2853 time to fit residues: 118.2079 Evaluate side-chains 296 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 245 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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 184 LEU 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 58 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 47 LEU 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 65 SER 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 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 34 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 231 GLU 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 L residue 89 CYS Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 545 GLU Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain F residue 577 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 114 optimal weight: 0.5980 chunk 88 optimal weight: 0.2980 chunk 131 optimal weight: 30.0000 chunk 87 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13764 Z= 0.335 Angle : 0.691 9.586 18678 Z= 0.338 Chirality : 0.048 0.267 2166 Planarity : 0.005 0.055 2337 Dihedral : 9.742 66.873 2667 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.01 % Favored : 96.62 % Rotamer: Outliers : 4.55 % Allowed : 13.56 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1629 helix: 1.64 (0.41), residues: 174 sheet: -0.91 (0.19), residues: 678 loop : -0.26 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 39 HIS 0.004 0.001 HIS F 549 PHE 0.015 0.002 PHE I 30 TYR 0.018 0.002 TYR G 99 ARG 0.009 0.001 ARG E 587 *********************** 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 316 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 253 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6613 (m-10) REVERT: A 100 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: A 184 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8891 (pp) REVERT: A 231 GLU cc_start: 0.8667 (mp0) cc_final: 0.8063 (mp0) REVERT: G 33 LYS cc_start: 0.5158 (OUTLIER) cc_final: 0.4209 (mttm) REVERT: J 32 LYS cc_start: 0.8389 (pttt) cc_final: 0.8056 (mmtt) REVERT: J 61 ASP cc_start: 0.7072 (p0) cc_final: 0.6711 (t0) REVERT: J 79 LEU cc_start: 0.6622 (tp) cc_final: 0.5852 (tt) REVERT: J 80 GLU cc_start: 0.5618 (mm-30) cc_final: 0.5267 (tp30) REVERT: D 510 LYS cc_start: 0.8832 (ptpt) cc_final: 0.7336 (mmtt) REVERT: D 565 THR cc_start: 0.8734 (p) cc_final: 0.8448 (t) REVERT: D 587 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8098 (mtp-110) REVERT: D 597 TRP cc_start: 0.6572 (m-90) cc_final: 0.6086 (m100) REVERT: B 100 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7750 (mp0) REVERT: B 231 GLU cc_start: 0.8325 (mp0) cc_final: 0.7891 (mp0) REVERT: B 261 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8198 (m-80) REVERT: H 87 GLN cc_start: 0.5565 (tp40) cc_final: 0.4721 (pm20) REVERT: H 99 TYR cc_start: 0.6721 (m-80) cc_final: 0.6411 (m-80) REVERT: H 100 TYR cc_start: 0.5461 (m-80) cc_final: 0.5223 (m-80) REVERT: K 32 LYS cc_start: 0.8046 (ptmm) cc_final: 0.7668 (mmtt) REVERT: K 61 ASP cc_start: 0.7074 (p0) cc_final: 0.6723 (t0) REVERT: K 80 GLU cc_start: 0.5110 (mm-30) cc_final: 0.4842 (tp30) REVERT: K 92 TYR cc_start: 0.4782 (OUTLIER) cc_final: 0.4384 (m-80) REVERT: E 510 LYS cc_start: 0.8880 (ptpt) cc_final: 0.7499 (mmtt) REVERT: E 551 GLN cc_start: 0.8691 (tp40) cc_final: 0.8206 (tp40) REVERT: E 597 TRP cc_start: 0.6351 (m-90) cc_final: 0.5931 (m100) REVERT: C 99 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.5843 (m-10) REVERT: C 100 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7400 (mp0) REVERT: C 217 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8545 (t) REVERT: C 231 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: C 261 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8204 (m-80) REVERT: I 19 ARG cc_start: 0.6174 (ttm170) cc_final: 0.5219 (ptm-80) REVERT: I 87 GLN cc_start: 0.5838 (tp40) cc_final: 0.5063 (mp10) REVERT: L 61 ASP cc_start: 0.7123 (p0) cc_final: 0.6755 (t0) REVERT: L 90 HIS cc_start: 0.6913 (t-90) cc_final: 0.6112 (t-170) REVERT: F 510 LYS cc_start: 0.8782 (ptpt) cc_final: 0.7318 (mmtt) REVERT: F 551 GLN cc_start: 0.8468 (tp40) cc_final: 0.8195 (tp40) REVERT: F 565 THR cc_start: 0.8968 (p) cc_final: 0.8576 (t) REVERT: F 578 GLU cc_start: 0.7929 (tt0) cc_final: 0.7668 (tt0) REVERT: F 587 ARG cc_start: 0.8378 (ttm110) cc_final: 0.8090 (mtp-110) REVERT: F 597 TRP cc_start: 0.6434 (m-90) cc_final: 0.5906 (m100) outliers start: 63 outliers final: 45 residues processed: 294 average time/residue: 0.2710 time to fit residues: 111.9635 Evaluate side-chains 305 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 250 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 184 LEU Chi-restraints excluded: chain A residue 247 ARG 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 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 47 LEU 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 65 SER 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 K residue 34 LEU Chi-restraints excluded: chain K residue 76 ILE 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 65 SER 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 217 THR Chi-restraints excluded: chain C residue 231 GLU 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 32 LYS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 545 GLU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 577 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 47 optimal weight: 0.0170 chunk 30 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 43 GLN C 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13764 Z= 0.311 Angle : 0.682 9.347 18678 Z= 0.333 Chirality : 0.049 0.408 2166 Planarity : 0.005 0.053 2337 Dihedral : 9.471 61.984 2667 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.07 % Favored : 96.56 % Rotamer: Outliers : 4.83 % Allowed : 14.07 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.21), residues: 1629 helix: 1.46 (0.40), residues: 180 sheet: -0.91 (0.20), residues: 657 loop : -0.34 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP L 36 HIS 0.005 0.001 HIS D 549 PHE 0.018 0.001 PHE I 30 TYR 0.020 0.002 TYR L 50 ARG 0.012 0.001 ARG E 587 *********************** 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 319 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 252 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6397 (m-10) REVERT: A 100 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: A 184 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8878 (pp) REVERT: A 231 GLU cc_start: 0.8664 (mp0) cc_final: 0.8096 (mp0) REVERT: G 33 LYS cc_start: 0.5255 (OUTLIER) cc_final: 0.4324 (mttm) REVERT: G 54 ILE cc_start: 0.5475 (OUTLIER) cc_final: 0.5204 (tt) REVERT: J 32 LYS cc_start: 0.8388 (pttt) cc_final: 0.8059 (mmtt) REVERT: J 61 ASP cc_start: 0.7041 (p0) cc_final: 0.6676 (t0) REVERT: J 79 LEU cc_start: 0.6613 (tp) cc_final: 0.5827 (tt) REVERT: J 80 GLU cc_start: 0.5597 (mm-30) cc_final: 0.5241 (tp30) REVERT: D 510 LYS cc_start: 0.8808 (ptpt) cc_final: 0.7340 (mmtt) REVERT: D 565 THR cc_start: 0.8716 (p) cc_final: 0.8431 (t) REVERT: D 587 ARG cc_start: 0.8380 (ttm110) cc_final: 0.8085 (mtp-110) REVERT: D 597 TRP cc_start: 0.6585 (m-90) cc_final: 0.6092 (m100) REVERT: B 100 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7751 (mp0) REVERT: B 130 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7835 (mtm-85) REVERT: B 217 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8609 (t) REVERT: B 231 GLU cc_start: 0.8302 (mp0) cc_final: 0.7829 (mp0) REVERT: B 261 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: H 87 GLN cc_start: 0.5563 (tp40) cc_final: 0.4727 (pm20) REVERT: H 99 TYR cc_start: 0.6777 (m-80) cc_final: 0.6495 (m-80) REVERT: H 100 TYR cc_start: 0.5605 (m-80) cc_final: 0.5345 (m-80) REVERT: K 32 LYS cc_start: 0.8050 (ptmm) cc_final: 0.7686 (mmtt) REVERT: K 61 ASP cc_start: 0.7075 (p0) cc_final: 0.6703 (t0) REVERT: K 80 GLU cc_start: 0.5231 (mm-30) cc_final: 0.4905 (tp30) REVERT: K 92 TYR cc_start: 0.4769 (OUTLIER) cc_final: 0.4396 (m-80) REVERT: E 510 LYS cc_start: 0.8859 (ptpt) cc_final: 0.7433 (mmtt) REVERT: E 551 GLN cc_start: 0.8709 (tp40) cc_final: 0.8223 (tp40) REVERT: E 587 ARG cc_start: 0.8288 (ttm110) cc_final: 0.7990 (mtp-110) REVERT: E 597 TRP cc_start: 0.6311 (m-90) cc_final: 0.5932 (m100) REVERT: C 99 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.5863 (m-10) REVERT: C 100 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7334 (mp0) REVERT: C 217 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8536 (t) REVERT: C 231 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: C 261 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: I 19 ARG cc_start: 0.6121 (ttm170) cc_final: 0.5066 (ptm-80) REVERT: I 87 GLN cc_start: 0.5704 (tp40) cc_final: 0.4975 (mp10) REVERT: I 99 TYR cc_start: 0.6585 (m-80) cc_final: 0.6262 (m-80) REVERT: L 61 ASP cc_start: 0.7071 (p0) cc_final: 0.6676 (t0) REVERT: L 90 HIS cc_start: 0.6861 (t-90) cc_final: 0.6060 (t-170) REVERT: F 510 LYS cc_start: 0.8776 (ptpt) cc_final: 0.7324 (mmtt) REVERT: F 551 GLN cc_start: 0.8480 (tp40) cc_final: 0.8240 (tp40) REVERT: F 565 THR cc_start: 0.8969 (p) cc_final: 0.8570 (t) REVERT: F 578 GLU cc_start: 0.7904 (tt0) cc_final: 0.7629 (tt0) REVERT: F 587 ARG cc_start: 0.8414 (ttm110) cc_final: 0.8079 (mtp-110) REVERT: F 597 TRP cc_start: 0.6290 (m-90) cc_final: 0.5765 (m100) outliers start: 67 outliers final: 48 residues processed: 294 average time/residue: 0.2699 time to fit residues: 111.5072 Evaluate side-chains 306 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 245 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 184 LEU Chi-restraints excluded: chain A residue 217 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 47 LEU 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 65 SER 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 217 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 121 ASP Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 76 ILE 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 65 SER 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 C residue 217 THR Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 545 GLU Chi-restraints excluded: chain F residue 547 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 149 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 145 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 114 optimal weight: 0.5980 chunk 44 optimal weight: 9.9990 chunk 131 optimal weight: 30.0000 chunk 137 optimal weight: 0.2980 chunk 144 optimal weight: 0.0980 chunk 95 optimal weight: 9.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13764 Z= 0.178 Angle : 0.650 12.859 18678 Z= 0.315 Chirality : 0.046 0.253 2166 Planarity : 0.005 0.055 2337 Dihedral : 8.855 57.293 2667 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.52 % Favored : 97.11 % Rotamer: Outliers : 3.61 % Allowed : 15.30 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1629 helix: 1.81 (0.40), residues: 180 sheet: -0.76 (0.20), residues: 657 loop : -0.34 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP L 36 HIS 0.003 0.001 HIS K 90 PHE 0.021 0.001 PHE J 72 TYR 0.022 0.001 TYR J 50 ARG 0.011 0.001 ARG E 587 *********************** 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 308 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 258 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: A 184 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8714 (pt) REVERT: A 231 GLU cc_start: 0.8568 (mp0) cc_final: 0.8015 (mp0) REVERT: G 33 LYS cc_start: 0.5184 (OUTLIER) cc_final: 0.4128 (mttt) REVERT: G 54 ILE cc_start: 0.5556 (OUTLIER) cc_final: 0.5262 (tt) REVERT: J 32 LYS cc_start: 0.8487 (pttt) cc_final: 0.8147 (mmtt) REVERT: J 61 ASP cc_start: 0.7112 (p0) cc_final: 0.6712 (t0) REVERT: J 79 LEU cc_start: 0.6594 (tp) cc_final: 0.5865 (tt) REVERT: J 80 GLU cc_start: 0.5770 (mm-30) cc_final: 0.5448 (tp30) REVERT: D 510 LYS cc_start: 0.8751 (ptpt) cc_final: 0.7271 (mmtt) REVERT: D 565 THR cc_start: 0.8733 (p) cc_final: 0.8471 (t) REVERT: D 587 ARG cc_start: 0.8381 (ttm110) cc_final: 0.8062 (mtp-110) REVERT: D 597 TRP cc_start: 0.6418 (m-90) cc_final: 0.5959 (m100) REVERT: B 100 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7556 (mp0) REVERT: B 130 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7891 (mtm-85) REVERT: B 217 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8530 (t) REVERT: B 231 GLU cc_start: 0.8255 (mp0) cc_final: 0.7799 (mp0) REVERT: B 261 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: H 37 MET cc_start: 0.6411 (mtt) cc_final: 0.6103 (mtt) REVERT: H 87 GLN cc_start: 0.5728 (tp40) cc_final: 0.5003 (pm20) REVERT: H 99 TYR cc_start: 0.6728 (m-80) cc_final: 0.6503 (m-80) REVERT: H 100 TYR cc_start: 0.5414 (m-80) cc_final: 0.5158 (m-80) REVERT: K 32 LYS cc_start: 0.8074 (ptmm) cc_final: 0.7682 (mmtt) REVERT: K 61 ASP cc_start: 0.7240 (p0) cc_final: 0.6903 (t0) REVERT: K 80 GLU cc_start: 0.5269 (mm-30) cc_final: 0.4931 (tp30) REVERT: E 510 LYS cc_start: 0.8837 (ptpt) cc_final: 0.7426 (mmtt) REVERT: E 551 GLN cc_start: 0.8696 (tp40) cc_final: 0.8219 (tp40) REVERT: E 587 ARG cc_start: 0.8274 (ttm110) cc_final: 0.7984 (mtp-110) REVERT: E 597 TRP cc_start: 0.6262 (m-90) cc_final: 0.5767 (m100) REVERT: C 100 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7146 (mp0) REVERT: C 231 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: C 261 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8385 (m-80) REVERT: I 19 ARG cc_start: 0.6016 (ttm170) cc_final: 0.5188 (ttp80) REVERT: I 87 GLN cc_start: 0.5759 (tp40) cc_final: 0.5061 (mp10) REVERT: I 99 TYR cc_start: 0.6564 (m-80) cc_final: 0.6206 (m-80) REVERT: L 37 TYR cc_start: 0.7029 (m-80) cc_final: 0.6400 (m-80) REVERT: L 61 ASP cc_start: 0.7230 (p0) cc_final: 0.6873 (t0) REVERT: L 90 HIS cc_start: 0.7021 (t-90) cc_final: 0.6019 (t70) REVERT: F 510 LYS cc_start: 0.8727 (ptpt) cc_final: 0.7267 (mmtt) REVERT: F 551 GLN cc_start: 0.8464 (tp40) cc_final: 0.8143 (tp40) REVERT: F 565 THR cc_start: 0.8982 (p) cc_final: 0.8619 (t) REVERT: F 578 GLU cc_start: 0.7774 (tt0) cc_final: 0.7461 (tt0) REVERT: F 587 ARG cc_start: 0.8400 (ttm110) cc_final: 0.8194 (mtp-110) REVERT: F 597 TRP cc_start: 0.6236 (m-90) cc_final: 0.5713 (m100) outliers start: 50 outliers final: 34 residues processed: 290 average time/residue: 0.2788 time to fit residues: 113.1140 Evaluate side-chains 288 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 245 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 184 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 239 LEU 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 J residue 76 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain B residue 65 SER 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 B residue 217 THR Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL 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 H residue 121 ASP Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS 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 153 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 0.0670 chunk 78 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13764 Z= 0.251 Angle : 0.691 10.643 18678 Z= 0.337 Chirality : 0.049 0.572 2166 Planarity : 0.005 0.052 2337 Dihedral : 8.682 59.887 2667 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.07 % Favored : 96.56 % Rotamer: Outliers : 3.39 % Allowed : 15.37 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1629 helix: 1.77 (0.40), residues: 180 sheet: -0.82 (0.20), residues: 660 loop : -0.35 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP L 36 HIS 0.004 0.001 HIS D 549 PHE 0.024 0.001 PHE J 72 TYR 0.020 0.002 TYR L 50 ARG 0.012 0.000 ARG E 587 ********************** 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 295 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 248 time to evaluate : 1.616 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: A 100 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: A 184 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8701 (pt) REVERT: A 231 GLU cc_start: 0.8547 (mp0) cc_final: 0.7975 (mp0) REVERT: A 261 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: G 33 LYS cc_start: 0.5141 (OUTLIER) cc_final: 0.4102 (mttt) REVERT: G 54 ILE cc_start: 0.5666 (OUTLIER) cc_final: 0.5351 (tt) REVERT: G 123 ILE cc_start: 0.7350 (mm) cc_final: 0.6684 (mm) REVERT: J 32 LYS cc_start: 0.8613 (pttt) cc_final: 0.8202 (mmtt) REVERT: J 61 ASP cc_start: 0.7054 (p0) cc_final: 0.6615 (t0) REVERT: J 79 LEU cc_start: 0.6602 (tp) cc_final: 0.5873 (tt) REVERT: J 80 GLU cc_start: 0.5848 (mm-30) cc_final: 0.5518 (tp30) REVERT: D 510 LYS cc_start: 0.8793 (ptpt) cc_final: 0.7316 (mmtt) REVERT: D 565 THR cc_start: 0.8796 (p) cc_final: 0.8513 (t) REVERT: D 587 ARG cc_start: 0.8375 (ttm110) cc_final: 0.8069 (mtp-110) REVERT: D 597 TRP cc_start: 0.6489 (m-90) cc_final: 0.6026 (m100) REVERT: B 100 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7727 (mp0) REVERT: B 130 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7838 (mtm-85) REVERT: B 217 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8542 (t) REVERT: B 231 GLU cc_start: 0.8205 (mp0) cc_final: 0.7773 (mp0) REVERT: B 261 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.8341 (m-80) REVERT: H 37 MET cc_start: 0.6473 (mtt) cc_final: 0.6137 (mtt) REVERT: H 99 TYR cc_start: 0.6693 (m-80) cc_final: 0.6416 (m-80) REVERT: H 100 TYR cc_start: 0.5418 (m-80) cc_final: 0.5158 (m-80) REVERT: K 32 LYS cc_start: 0.8098 (ptmm) cc_final: 0.7703 (mmtt) REVERT: K 61 ASP cc_start: 0.7242 (p0) cc_final: 0.6893 (t0) REVERT: K 80 GLU cc_start: 0.5443 (mm-30) cc_final: 0.5078 (tp30) REVERT: E 510 LYS cc_start: 0.8849 (ptpt) cc_final: 0.7423 (mmtt) REVERT: E 551 GLN cc_start: 0.8698 (tp40) cc_final: 0.8225 (tp40) REVERT: E 587 ARG cc_start: 0.8309 (ttm110) cc_final: 0.8021 (mtp-110) REVERT: E 597 TRP cc_start: 0.6329 (m-90) cc_final: 0.5903 (m100) REVERT: C 100 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7226 (mp0) REVERT: C 231 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: C 261 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: I 19 ARG cc_start: 0.6071 (ttm170) cc_final: 0.5177 (ttp80) REVERT: I 87 GLN cc_start: 0.5653 (tp40) cc_final: 0.4922 (mp10) REVERT: I 99 TYR cc_start: 0.6613 (m-80) cc_final: 0.6268 (m-80) REVERT: L 37 TYR cc_start: 0.7000 (m-80) cc_final: 0.6323 (m-80) REVERT: L 61 ASP cc_start: 0.7229 (p0) cc_final: 0.6858 (t0) REVERT: L 90 HIS cc_start: 0.7050 (t-90) cc_final: 0.6098 (t70) REVERT: F 510 LYS cc_start: 0.8742 (ptpt) cc_final: 0.7280 (mmtt) REVERT: F 551 GLN cc_start: 0.8469 (tp40) cc_final: 0.8137 (tp40) REVERT: F 565 THR cc_start: 0.8992 (p) cc_final: 0.8590 (t) REVERT: F 578 GLU cc_start: 0.7767 (tt0) cc_final: 0.7510 (tt0) REVERT: F 587 ARG cc_start: 0.8462 (ttm110) cc_final: 0.8195 (mtp-110) REVERT: F 597 TRP cc_start: 0.6281 (m-90) cc_final: 0.5765 (m100) outliers start: 47 outliers final: 33 residues processed: 278 average time/residue: 0.2919 time to fit residues: 113.4506 Evaluate side-chains 287 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 244 time to evaluate : 1.557 ------------------------------------------------------------------------------- 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 184 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 247 ARG 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 J residue 76 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain B residue 65 SER 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 B residue 217 THR Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain F residue 547 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 136 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 118 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 113 optimal weight: 0.2980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 595 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 = 0.3708 r_free = 0.3708 target = 0.138382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.111751 restraints weight = 21398.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.111029 restraints weight = 57434.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111466 restraints weight = 49735.013| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13764 Z= 0.343 Angle : 0.726 12.323 18678 Z= 0.355 Chirality : 0.049 0.457 2166 Planarity : 0.005 0.055 2337 Dihedral : 8.119 58.829 2667 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.25 % Favored : 96.38 % Rotamer: Outliers : 3.54 % Allowed : 15.30 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.21), residues: 1629 helix: 1.58 (0.40), residues: 180 sheet: -0.97 (0.19), residues: 666 loop : -0.38 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP L 36 HIS 0.005 0.001 HIS D 549 PHE 0.021 0.002 PHE J 72 TYR 0.023 0.002 TYR J 50 ARG 0.022 0.001 ARG K 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2988.31 seconds wall clock time: 54 minutes 24.19 seconds (3264.19 seconds total)