Starting phenix.real_space_refine on Thu Jul 31 16:30:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kfb_22848/07_2025/7kfb_22848.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kfb_22848/07_2025/7kfb_22848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kfb_22848/07_2025/7kfb_22848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kfb_22848/07_2025/7kfb_22848.map" model { file = "/net/cci-nas-00/data/ceres_data/7kfb_22848/07_2025/7kfb_22848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kfb_22848/07_2025/7kfb_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.12, 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=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.04 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 101 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.02 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.05 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 101 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 101 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.02 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.05 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 5 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 401 " - " ASN A 268 " " NAG A 402 " - " ASN A 238 " " NAG B 401 " - " ASN B 268 " " NAG B 402 " - " ASN B 238 " " NAG C 401 " - " ASN C 268 " " NAG C 402 " - " ASN C 238 " " NAG M 1 " - " ASN A 257 " " NAG N 1 " - " ASN A 228 " " NAG O 1 " - " ASN D 563 " " NAG P 1 " - " ASN B 257 " " NAG Q 1 " - " ASN B 228 " " NAG R 1 " - " ASN E 563 " " NAG S 1 " - " ASN C 257 " " NAG T 1 " - " ASN C 228 " " NAG U 1 " - " ASN F 563 " Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.6 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: 2.18 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: 5.01 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2537 1.32 - 1.46: 4800 1.46 - 1.60: 6340 1.60 - 1.74: 48 1.74 - 1.87: 39 Bond restraints: 13764 Sorted by residual: bond pdb=" CB TYR C 99 " pdb=" CG TYR C 99 " ideal model delta sigma weight residual 1.512 1.331 0.181 2.20e-02 2.07e+03 6.77e+01 bond pdb=" CB TYR A 99 " pdb=" CG TYR A 99 " ideal model delta sigma weight residual 1.512 1.331 0.181 2.20e-02 2.07e+03 6.77e+01 bond pdb=" CB TYR B 99 " pdb=" CG TYR B 99 " ideal model delta sigma weight residual 1.512 1.331 0.181 2.20e-02 2.07e+03 6.74e+01 bond pdb=" CB ILE L 107 " pdb=" CG1 ILE L 107 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" CB ILE K 107 " pdb=" CG1 ILE K 107 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 13759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 15397 2.26 - 4.53: 2687 4.53 - 6.79: 495 6.79 - 9.05: 84 9.05 - 11.31: 15 Bond angle restraints: 18678 Sorted by residual: angle pdb=" CA ASP H 78 " pdb=" CB ASP H 78 " pdb=" CG ASP H 78 " ideal model delta sigma weight residual 112.60 120.73 -8.13 1.00e+00 1.00e+00 6.61e+01 angle pdb=" CA ASP I 78 " pdb=" CB ASP I 78 " pdb=" CG ASP I 78 " ideal model delta sigma weight residual 112.60 120.70 -8.10 1.00e+00 1.00e+00 6.56e+01 angle pdb=" CA ASP G 78 " pdb=" CB ASP G 78 " pdb=" CG ASP G 78 " ideal model delta sigma weight residual 112.60 120.70 -8.10 1.00e+00 1.00e+00 6.56e+01 angle pdb=" N LEU A 186 " pdb=" CA LEU A 186 " pdb=" C LEU A 186 " ideal model delta sigma weight residual 113.16 124.47 -11.31 1.42e+00 4.96e-01 6.35e+01 angle pdb=" N LEU B 186 " pdb=" CA LEU B 186 " pdb=" C LEU B 186 " ideal model delta sigma weight residual 113.16 124.44 -11.28 1.42e+00 4.96e-01 6.31e+01 ... (remaining 18673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 8322 21.39 - 42.78: 183 42.78 - 64.16: 54 64.16 - 85.55: 45 85.55 - 106.94: 24 Dihedral angle restraints: 8628 sinusoidal: 3918 harmonic: 4710 Sorted by residual: dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 101 " pdb=" CB CYS I 101 " ideal model delta sinusoidal sigma weight residual 93.00 32.54 60.46 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 101 " pdb=" CB CYS G 101 " ideal model delta sinusoidal sigma weight residual 93.00 32.60 60.40 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 101 " pdb=" CB CYS H 101 " ideal model delta sinusoidal sigma weight residual 93.00 32.61 60.39 1 1.00e+01 1.00e-02 4.86e+01 ... (remaining 8625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1462 0.105 - 0.210: 510 0.210 - 0.315: 130 0.315 - 0.420: 47 0.420 - 0.525: 17 Chirality restraints: 2166 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.71e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.65e+01 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.62e+01 ... (remaining 2163 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 99 " -0.105 2.00e-02 2.50e+03 5.64e-02 6.36e+01 pdb=" CG TYR B 99 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 99 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR B 99 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR B 99 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR B 99 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR B 99 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 99 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 99 " -0.104 2.00e-02 2.50e+03 5.62e-02 6.31e+01 pdb=" CG TYR C 99 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 99 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR C 99 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR C 99 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR C 99 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR C 99 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 99 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 99 " 0.104 2.00e-02 2.50e+03 5.61e-02 6.28e+01 pdb=" CG TYR A 99 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 99 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR A 99 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR A 99 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 99 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 99 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 99 " 0.083 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 6795 2.97 - 3.45: 11904 3.45 - 3.93: 22990 3.93 - 4.42: 26331 4.42 - 4.90: 41881 Nonbonded interactions: 109901 Sorted by model distance: nonbonded pdb=" O LEU L 34 " pdb=" N GLY L 51 " model vdw 2.486 3.120 nonbonded pdb=" O LEU J 34 " pdb=" N GLY J 51 " model vdw 2.487 3.120 nonbonded pdb=" N TYR B 162 " pdb=" O TYR B 162 " model vdw 2.487 2.496 nonbonded pdb=" N TYR A 162 " pdb=" O TYR A 162 " model vdw 2.487 2.496 nonbonded pdb=" N TYR C 162 " pdb=" O TYR C 162 " model vdw 2.487 2.496 ... (remaining 109896 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 32.930 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.181 13821 Z= 1.153 Angle : 1.878 12.662 18834 Z= 1.212 Chirality : 0.125 0.525 2166 Planarity : 0.009 0.060 2337 Dihedral : 13.131 106.938 5601 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.55 % Allowed : 1.29 % Favored : 98.16 % Rotamer: Outliers : 0.22 % Allowed : 1.73 % Favored : 98.05 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd link_NAG-ASN : bond 0.07781 ( 15) link_NAG-ASN : angle 2.17193 ( 45) link_ALPHA1-6 : bond 0.06484 ( 6) link_ALPHA1-6 : angle 3.69408 ( 18) link_BETA1-4 : bond 0.07461 ( 15) link_BETA1-4 : angle 5.47075 ( 45) link_ALPHA1-3 : bond 0.08211 ( 6) link_ALPHA1-3 : angle 4.43956 ( 18) hydrogen bonds : bond 0.16687 ( 489) hydrogen bonds : angle 8.08626 ( 1251) SS BOND : bond 0.01210 ( 15) SS BOND : angle 3.20523 ( 30) covalent geometry : bond 0.02208 (13764) covalent geometry : angle 1.85072 (18678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 402 time to evaluate : 1.601 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: 0.3165 time to fit residues: 172.4061 Evaluate side-chains 260 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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: 0.6980 chunk 126 optimal weight: 0.8980 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: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120776 restraints weight = 21254.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120230 restraints weight = 53539.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118945 restraints weight = 43364.831| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13821 Z= 0.201 Angle : 0.857 20.014 18834 Z= 0.413 Chirality : 0.050 0.237 2166 Planarity : 0.005 0.045 2337 Dihedral : 12.748 90.951 2667 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.09 % Favored : 97.73 % Rotamer: Outliers : 2.02 % Allowed : 9.09 % Favored : 88.89 % 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: 0.34 (0.21), residues: 1629 helix: 2.58 (0.36), residues: 150 sheet: -0.39 (0.19), residues: 705 loop : 0.57 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 36 HIS 0.003 0.001 HIS E 549 PHE 0.038 0.002 PHE J 72 TYR 0.022 0.002 TYR H 118 ARG 0.009 0.001 ARG E 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00934 ( 15) link_NAG-ASN : angle 6.38865 ( 45) link_ALPHA1-6 : bond 0.01046 ( 6) link_ALPHA1-6 : angle 1.82361 ( 18) link_BETA1-4 : bond 0.02067 ( 15) link_BETA1-4 : angle 4.65356 ( 45) link_ALPHA1-3 : bond 0.01714 ( 6) link_ALPHA1-3 : angle 0.84935 ( 18) hydrogen bonds : bond 0.05297 ( 489) hydrogen bonds : angle 6.21778 ( 1251) SS BOND : bond 0.00411 ( 15) SS BOND : angle 1.42165 ( 30) covalent geometry : bond 0.00447 (13764) covalent geometry : angle 0.76336 (18678) *********************** 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 308 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6850 (mp0) REVERT: J 80 GLU cc_start: 0.5962 (mm-30) cc_final: 0.5673 (tp30) REVERT: D 510 LYS cc_start: 0.8472 (ptpt) cc_final: 0.7357 (mmtt) REVERT: D 565 THR cc_start: 0.8550 (p) cc_final: 0.8151 (t) REVERT: D 597 TRP cc_start: 0.6290 (m-90) cc_final: 0.5814 (m100) REVERT: E 510 LYS cc_start: 0.8608 (ptpt) cc_final: 0.7507 (mmtt) REVERT: E 565 THR cc_start: 0.8762 (p) cc_final: 0.8448 (t) REVERT: E 578 GLU cc_start: 0.7450 (tt0) cc_final: 0.7226 (tt0) REVERT: E 597 TRP cc_start: 0.6349 (m-90) cc_final: 0.5852 (m100) REVERT: C 100 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6882 (mp0) REVERT: F 510 LYS cc_start: 0.8581 (ptpt) cc_final: 0.7515 (mmtt) REVERT: F 565 THR cc_start: 0.8767 (p) cc_final: 0.8359 (t) REVERT: F 597 TRP cc_start: 0.6213 (m-90) cc_final: 0.5806 (m100) outliers start: 28 outliers final: 23 residues processed: 294 average time/residue: 0.2885 time to fit residues: 117.7541 Evaluate side-chains 268 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 260 ILE 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 B residue 65 SER 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 260 ILE 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 24 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 C 243 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.141368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.110933 restraints weight = 21707.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.110944 restraints weight = 57439.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110969 restraints weight = 45019.433| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13821 Z= 0.226 Angle : 0.783 14.713 18834 Z= 0.376 Chirality : 0.049 0.245 2166 Planarity : 0.005 0.045 2337 Dihedral : 11.439 84.411 2667 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.96 % Favored : 97.85 % Rotamer: Outliers : 3.39 % Allowed : 11.83 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.16 (0.21), residues: 1629 helix: 1.37 (0.38), residues: 174 sheet: -0.71 (0.19), residues: 699 loop : 0.38 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 36 HIS 0.006 0.002 HIS K 90 PHE 0.020 0.002 PHE J 72 TYR 0.021 0.002 TYR G 100 ARG 0.009 0.001 ARG E 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 15) link_NAG-ASN : angle 4.07610 ( 45) link_ALPHA1-6 : bond 0.00802 ( 6) link_ALPHA1-6 : angle 1.86500 ( 18) link_BETA1-4 : bond 0.01697 ( 15) link_BETA1-4 : angle 3.82085 ( 45) link_ALPHA1-3 : bond 0.01663 ( 6) link_ALPHA1-3 : angle 1.02056 ( 18) hydrogen bonds : bond 0.04759 ( 489) hydrogen bonds : angle 5.75362 ( 1251) SS BOND : bond 0.00314 ( 15) SS BOND : angle 1.31029 ( 30) covalent geometry : bond 0.00529 (13764) covalent geometry : angle 0.73158 (18678) *********************** 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 308 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 261 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: J 37 TYR cc_start: 0.6902 (m-80) cc_final: 0.6698 (m-80) REVERT: D 510 LYS cc_start: 0.8602 (ptpt) cc_final: 0.7323 (mmtt) REVERT: D 551 GLN cc_start: 0.8189 (tp40) cc_final: 0.7598 (tp40) REVERT: D 565 THR cc_start: 0.8736 (p) cc_final: 0.8327 (t) REVERT: D 597 TRP cc_start: 0.6452 (m-90) cc_final: 0.5995 (m100) REVERT: B 130 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7284 (mtm-85) REVERT: H 33 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5044 (mttt) REVERT: K 32 LYS cc_start: 0.8231 (ptmm) cc_final: 0.7926 (mmtt) REVERT: E 510 LYS cc_start: 0.8677 (ptpt) cc_final: 0.7410 (mmtt) REVERT: E 565 THR cc_start: 0.8764 (p) cc_final: 0.8437 (t) REVERT: E 597 TRP cc_start: 0.6429 (m-90) cc_final: 0.5949 (m100) REVERT: C 231 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: C 261 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: F 510 LYS cc_start: 0.8641 (ptpt) cc_final: 0.7382 (mmtt) REVERT: F 551 GLN cc_start: 0.8227 (tp40) cc_final: 0.7904 (tp40) REVERT: F 565 THR cc_start: 0.8841 (p) cc_final: 0.8365 (t) REVERT: F 578 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7424 (tt0) REVERT: F 597 TRP cc_start: 0.6383 (m-90) cc_final: 0.5928 (m100) outliers start: 47 outliers final: 31 residues processed: 286 average time/residue: 0.2821 time to fit residues: 113.4366 Evaluate side-chains 280 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain B residue 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 B residue 144 THR 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 E residue 544 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 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 115 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 545 GLU Chi-restraints excluded: chain F residue 564 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 106 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 60 optimal weight: 0.0000 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.143216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119381 restraints weight = 21313.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118953 restraints weight = 54919.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117340 restraints weight = 46697.647| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13821 Z= 0.142 Angle : 0.695 12.476 18834 Z= 0.330 Chirality : 0.047 0.262 2166 Planarity : 0.005 0.071 2337 Dihedral : 10.433 77.351 2667 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.90 % Favored : 97.91 % Rotamer: Outliers : 3.03 % Allowed : 11.83 % Favored : 85.14 % 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: -0.08 (0.21), residues: 1629 helix: 1.65 (0.38), residues: 174 sheet: -0.59 (0.20), residues: 672 loop : 0.26 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 97 HIS 0.004 0.001 HIS K 90 PHE 0.014 0.001 PHE J 72 TYR 0.020 0.002 TYR L 92 ARG 0.010 0.001 ARG E 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 15) link_NAG-ASN : angle 3.66990 ( 45) link_ALPHA1-6 : bond 0.01039 ( 6) link_ALPHA1-6 : angle 1.97871 ( 18) link_BETA1-4 : bond 0.01618 ( 15) link_BETA1-4 : angle 3.40892 ( 45) link_ALPHA1-3 : bond 0.01611 ( 6) link_ALPHA1-3 : angle 1.07585 ( 18) hydrogen bonds : bond 0.03756 ( 489) hydrogen bonds : angle 5.39187 ( 1251) SS BOND : bond 0.00188 ( 15) SS BOND : angle 0.91413 ( 30) covalent geometry : bond 0.00306 (13764) covalent geometry : angle 0.64813 (18678) *********************** 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 306 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 1.437 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: A 99 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6148 (m-10) REVERT: J 32 LYS cc_start: 0.8341 (pttt) cc_final: 0.8073 (mmtt) REVERT: D 510 LYS cc_start: 0.8475 (ptpt) cc_final: 0.7269 (mmtt) REVERT: D 551 GLN cc_start: 0.8125 (tp40) cc_final: 0.7469 (tp40) REVERT: D 565 THR cc_start: 0.8721 (p) cc_final: 0.8316 (t) REVERT: D 597 TRP cc_start: 0.6381 (m-90) cc_final: 0.6010 (m100) REVERT: B 130 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7237 (mtm-85) REVERT: B 184 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8960 (pp) REVERT: B 261 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: K 92 TYR cc_start: 0.5263 (OUTLIER) cc_final: 0.5025 (m-80) REVERT: E 510 LYS cc_start: 0.8629 (ptpt) cc_final: 0.7340 (mmtt) REVERT: E 551 GLN cc_start: 0.8249 (tp40) cc_final: 0.7812 (tp40) REVERT: E 565 THR cc_start: 0.8774 (p) cc_final: 0.8519 (t) REVERT: C 99 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.6107 (m-10) REVERT: C 261 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: F 510 LYS cc_start: 0.8528 (ptpt) cc_final: 0.7181 (mmtt) REVERT: F 565 THR cc_start: 0.8850 (p) cc_final: 0.8377 (t) REVERT: F 597 TRP cc_start: 0.6257 (m-90) cc_final: 0.5878 (m100) outliers start: 42 outliers final: 28 residues processed: 290 average time/residue: 0.2806 time to fit residues: 114.1548 Evaluate side-chains 277 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 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 119 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 142 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 13 optimal weight: 0.0030 chunk 55 optimal weight: 0.0270 overall best weight: 0.4448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 3 GLN K 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112560 restraints weight = 21425.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103925 restraints weight = 25130.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.104221 restraints weight = 38604.158| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13821 Z= 0.125 Angle : 0.669 10.737 18834 Z= 0.317 Chirality : 0.046 0.262 2166 Planarity : 0.004 0.064 2337 Dihedral : 9.838 72.211 2667 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.46 % Favored : 97.30 % Rotamer: Outliers : 3.10 % Allowed : 12.48 % Favored : 84.42 % 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: -0.17 (0.21), residues: 1629 helix: 1.87 (0.38), residues: 174 sheet: -0.65 (0.19), residues: 708 loop : 0.16 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP J 36 HIS 0.005 0.001 HIS K 90 PHE 0.033 0.001 PHE E 592 TYR 0.020 0.002 TYR G 100 ARG 0.010 0.000 ARG E 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 15) link_NAG-ASN : angle 3.06708 ( 45) link_ALPHA1-6 : bond 0.01080 ( 6) link_ALPHA1-6 : angle 1.95375 ( 18) link_BETA1-4 : bond 0.01544 ( 15) link_BETA1-4 : angle 3.23434 ( 45) link_ALPHA1-3 : bond 0.01659 ( 6) link_ALPHA1-3 : angle 1.19126 ( 18) hydrogen bonds : bond 0.03430 ( 489) hydrogen bonds : angle 5.17356 ( 1251) SS BOND : bond 0.00159 ( 15) SS BOND : angle 0.94350 ( 30) covalent geometry : bond 0.00262 (13764) covalent geometry : angle 0.62973 (18678) *********************** 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 292 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 1.463 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: A 99 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.6103 (m-10) REVERT: A 231 GLU cc_start: 0.7232 (mp0) cc_final: 0.6991 (mp0) REVERT: J 32 LYS cc_start: 0.8859 (pttt) cc_final: 0.8300 (mmtt) REVERT: D 510 LYS cc_start: 0.8525 (ptpt) cc_final: 0.7227 (mmtt) REVERT: D 551 GLN cc_start: 0.8187 (tp40) cc_final: 0.7658 (tp40) REVERT: D 565 THR cc_start: 0.8626 (p) cc_final: 0.8305 (t) REVERT: D 597 TRP cc_start: 0.6359 (m-90) cc_final: 0.5948 (m100) REVERT: B 130 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7279 (mtm-85) REVERT: B 261 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.8117 (m-80) REVERT: K 32 LYS cc_start: 0.8471 (ptmm) cc_final: 0.7918 (mmtt) REVERT: K 86 VAL cc_start: 0.7157 (p) cc_final: 0.6945 (p) REVERT: K 92 TYR cc_start: 0.5570 (OUTLIER) cc_final: 0.5128 (m-80) REVERT: E 510 LYS cc_start: 0.8638 (ptpt) cc_final: 0.7294 (mmtt) REVERT: E 565 THR cc_start: 0.8735 (p) cc_final: 0.8467 (t) REVERT: C 99 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.6208 (m-10) REVERT: C 261 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7909 (m-80) REVERT: C 265 LYS cc_start: 0.8605 (mttt) cc_final: 0.8395 (mttt) REVERT: F 510 LYS cc_start: 0.8515 (ptpt) cc_final: 0.7123 (mmtt) REVERT: F 565 THR cc_start: 0.8800 (p) cc_final: 0.8444 (t) REVERT: F 578 GLU cc_start: 0.7595 (tt0) cc_final: 0.7295 (tt0) REVERT: F 597 TRP cc_start: 0.6321 (m-90) cc_final: 0.5915 (m100) outliers start: 43 outliers final: 29 residues processed: 276 average time/residue: 0.2743 time to fit residues: 107.0411 Evaluate side-chains 271 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR 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 107 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 23 optimal weight: 50.0000 chunk 96 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 161 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.139503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112135 restraints weight = 21717.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110168 restraints weight = 57261.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110801 restraints weight = 49687.569| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13821 Z= 0.228 Angle : 0.747 11.331 18834 Z= 0.356 Chirality : 0.048 0.265 2166 Planarity : 0.005 0.062 2337 Dihedral : 9.760 69.057 2667 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.64 % Favored : 97.11 % Rotamer: Outliers : 3.97 % Allowed : 12.77 % Favored : 83.26 % 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: 1.48 (0.39), residues: 174 sheet: -0.82 (0.19), residues: 693 loop : -0.13 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 97 HIS 0.004 0.001 HIS K 90 PHE 0.016 0.002 PHE G 113 TYR 0.018 0.002 TYR G 100 ARG 0.012 0.001 ARG E 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 15) link_NAG-ASN : angle 2.71426 ( 45) link_ALPHA1-6 : bond 0.00903 ( 6) link_ALPHA1-6 : angle 2.02719 ( 18) link_BETA1-4 : bond 0.01472 ( 15) link_BETA1-4 : angle 3.46335 ( 45) link_ALPHA1-3 : bond 0.01534 ( 6) link_ALPHA1-3 : angle 1.39622 ( 18) hydrogen bonds : bond 0.04455 ( 489) hydrogen bonds : angle 5.24698 ( 1251) SS BOND : bond 0.00330 ( 15) SS BOND : angle 1.07072 ( 30) covalent geometry : bond 0.00544 (13764) covalent geometry : angle 0.71343 (18678) *********************** 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 297 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 1.462 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: 0.7141 (OUTLIER) cc_final: 0.6351 (m-10) REVERT: A 231 GLU cc_start: 0.7188 (mp0) cc_final: 0.6982 (mp0) REVERT: J 32 LYS cc_start: 0.8420 (pttt) cc_final: 0.8177 (mmtt) REVERT: D 510 LYS cc_start: 0.8642 (ptpt) cc_final: 0.7319 (mmtt) REVERT: D 565 THR cc_start: 0.8654 (p) cc_final: 0.8295 (t) REVERT: D 597 TRP cc_start: 0.6561 (m-90) cc_final: 0.6127 (m100) REVERT: B 130 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7262 (mtm-85) REVERT: B 155 LYS cc_start: 0.9031 (mttt) cc_final: 0.8816 (mttm) REVERT: B 231 GLU cc_start: 0.7182 (mp0) cc_final: 0.6922 (mp0) REVERT: B 261 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: E 510 LYS cc_start: 0.8717 (ptpt) cc_final: 0.7399 (mmtt) REVERT: E 551 GLN cc_start: 0.8312 (tp40) cc_final: 0.7890 (tp40) REVERT: E 565 THR cc_start: 0.8515 (p) cc_final: 0.8246 (t) REVERT: E 597 TRP cc_start: 0.6464 (m-90) cc_final: 0.6123 (m100) REVERT: C 99 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6254 (m-10) REVERT: C 184 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8859 (pp) REVERT: C 261 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.8173 (m-80) REVERT: I 121 ASP cc_start: 0.7091 (t70) cc_final: 0.6600 (t70) REVERT: F 510 LYS cc_start: 0.8584 (ptpt) cc_final: 0.7198 (mmtt) REVERT: F 551 GLN cc_start: 0.8169 (tp40) cc_final: 0.7932 (tp40) REVERT: F 565 THR cc_start: 0.8878 (p) cc_final: 0.8419 (t) REVERT: F 578 GLU cc_start: 0.7566 (tt0) cc_final: 0.7323 (tt0) REVERT: F 597 TRP cc_start: 0.6432 (m-90) cc_final: 0.5974 (m100) outliers start: 55 outliers final: 40 residues processed: 278 average time/residue: 0.2865 time to fit residues: 111.4368 Evaluate side-chains 283 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 103 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 227 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 E residue 544 THR Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 93 THR 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 79 LEU Chi-restraints excluded: chain F residue 544 THR 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 27 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.141239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.115557 restraints weight = 21549.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.113808 restraints weight = 56031.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.114256 restraints weight = 55683.340| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13821 Z= 0.146 Angle : 0.696 11.531 18834 Z= 0.328 Chirality : 0.047 0.259 2166 Planarity : 0.005 0.061 2337 Dihedral : 9.269 64.453 2667 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.27 % Favored : 97.48 % Rotamer: Outliers : 3.61 % Allowed : 13.42 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.44 (0.21), residues: 1629 helix: 1.76 (0.39), residues: 174 sheet: -0.76 (0.20), residues: 678 loop : -0.16 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 39 HIS 0.005 0.001 HIS K 90 PHE 0.023 0.001 PHE E 592 TYR 0.019 0.002 TYR J 50 ARG 0.012 0.001 ARG E 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 15) link_NAG-ASN : angle 3.50929 ( 45) link_ALPHA1-6 : bond 0.01037 ( 6) link_ALPHA1-6 : angle 1.99300 ( 18) link_BETA1-4 : bond 0.01547 ( 15) link_BETA1-4 : angle 3.25803 ( 45) link_ALPHA1-3 : bond 0.01637 ( 6) link_ALPHA1-3 : angle 1.40497 ( 18) hydrogen bonds : bond 0.03573 ( 489) hydrogen bonds : angle 5.08795 ( 1251) SS BOND : bond 0.00166 ( 15) SS BOND : angle 0.74638 ( 30) covalent geometry : bond 0.00326 (13764) covalent geometry : angle 0.65263 (18678) *********************** 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 301 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 251 time to evaluate : 1.609 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: 0.6951 (OUTLIER) cc_final: 0.6024 (m-10) REVERT: A 231 GLU cc_start: 0.7210 (mp0) cc_final: 0.6850 (mp0) REVERT: G 54 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6791 (tt) REVERT: J 32 LYS cc_start: 0.8407 (pttt) cc_final: 0.8176 (mmtt) REVERT: D 510 LYS cc_start: 0.8536 (ptpt) cc_final: 0.7230 (mmtt) REVERT: D 565 THR cc_start: 0.8583 (p) cc_final: 0.8268 (t) REVERT: D 597 TRP cc_start: 0.6526 (m-90) cc_final: 0.6054 (m100) REVERT: B 130 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7258 (mtm-85) REVERT: B 155 LYS cc_start: 0.9005 (mttt) cc_final: 0.8768 (mttm) REVERT: B 231 GLU cc_start: 0.7157 (mp0) cc_final: 0.6687 (mp0) REVERT: H 33 LYS cc_start: 0.5853 (OUTLIER) cc_final: 0.5119 (mttm) REVERT: K 92 TYR cc_start: 0.5473 (OUTLIER) cc_final: 0.5121 (m-80) REVERT: E 510 LYS cc_start: 0.8644 (ptpt) cc_final: 0.7273 (mmtt) REVERT: E 551 GLN cc_start: 0.8406 (tp40) cc_final: 0.7912 (tp40) REVERT: E 565 THR cc_start: 0.8712 (p) cc_final: 0.8469 (t) REVERT: E 597 TRP cc_start: 0.6444 (m-90) cc_final: 0.6013 (m100) REVERT: C 99 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6257 (m-10) REVERT: C 184 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8814 (pp) REVERT: I 121 ASP cc_start: 0.7078 (t70) cc_final: 0.6646 (t70) REVERT: F 510 LYS cc_start: 0.8505 (ptpt) cc_final: 0.7118 (mmtt) REVERT: F 551 GLN cc_start: 0.8159 (tp40) cc_final: 0.7925 (tp40) REVERT: F 565 THR cc_start: 0.8737 (p) cc_final: 0.8342 (t) REVERT: F 578 GLU cc_start: 0.7534 (tt0) cc_final: 0.7261 (tt0) REVERT: F 597 TRP cc_start: 0.6431 (m-90) cc_final: 0.5916 (m100) outliers start: 50 outliers final: 32 residues processed: 285 average time/residue: 0.2833 time to fit residues: 113.2022 Evaluate side-chains 281 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 227 THR 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 69 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 564 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 137 optimal weight: 9.9990 chunk 9 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.118484 restraints weight = 21637.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.118118 restraints weight = 55717.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115749 restraints weight = 41031.426| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13821 Z= 0.155 Angle : 0.708 13.857 18834 Z= 0.333 Chirality : 0.046 0.262 2166 Planarity : 0.005 0.066 2337 Dihedral : 9.009 60.841 2667 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.95 % Favored : 96.75 % Rotamer: Outliers : 3.75 % Allowed : 13.56 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.46 (0.21), residues: 1629 helix: 1.69 (0.39), residues: 177 sheet: -0.73 (0.20), residues: 654 loop : -0.24 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 36 HIS 0.004 0.001 HIS K 90 PHE 0.014 0.001 PHE K 72 TYR 0.017 0.002 TYR H 85 ARG 0.008 0.001 ARG E 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 15) link_NAG-ASN : angle 2.82663 ( 45) link_ALPHA1-6 : bond 0.01001 ( 6) link_ALPHA1-6 : angle 1.94902 ( 18) link_BETA1-4 : bond 0.01509 ( 15) link_BETA1-4 : angle 3.27872 ( 45) link_ALPHA1-3 : bond 0.01614 ( 6) link_ALPHA1-3 : angle 1.49586 ( 18) hydrogen bonds : bond 0.03652 ( 489) hydrogen bonds : angle 5.03089 ( 1251) SS BOND : bond 0.00218 ( 15) SS BOND : angle 0.86848 ( 30) covalent geometry : bond 0.00351 (13764) covalent geometry : angle 0.67359 (18678) *********************** 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 296 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.6108 (m-10) REVERT: A 231 GLU cc_start: 0.7162 (mp0) cc_final: 0.6868 (mp0) REVERT: G 33 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5024 (mmtp) REVERT: G 54 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.6764 (tt) REVERT: D 510 LYS cc_start: 0.8513 (ptpt) cc_final: 0.7207 (mmtt) REVERT: D 565 THR cc_start: 0.8616 (p) cc_final: 0.8265 (t) REVERT: D 597 TRP cc_start: 0.6457 (m-90) cc_final: 0.6050 (m100) REVERT: B 130 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7236 (mtm-85) REVERT: B 155 LYS cc_start: 0.9016 (mttt) cc_final: 0.8780 (mttm) REVERT: B 231 GLU cc_start: 0.7178 (mp0) cc_final: 0.6780 (mp0) REVERT: H 33 LYS cc_start: 0.5819 (OUTLIER) cc_final: 0.5092 (mttm) REVERT: K 48 LEU cc_start: 0.6297 (mp) cc_final: 0.5951 (mp) REVERT: K 92 TYR cc_start: 0.5522 (OUTLIER) cc_final: 0.5153 (m-80) REVERT: E 510 LYS cc_start: 0.8670 (ptpt) cc_final: 0.7305 (mmtt) REVERT: E 551 GLN cc_start: 0.8364 (tp40) cc_final: 0.7935 (tp40) REVERT: E 558 LEU cc_start: 0.8752 (tp) cc_final: 0.8550 (tp) REVERT: E 565 THR cc_start: 0.8729 (p) cc_final: 0.8473 (t) REVERT: E 597 TRP cc_start: 0.6375 (m-90) cc_final: 0.5969 (m100) REVERT: C 99 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.6210 (m-10) REVERT: C 184 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8659 (pp) REVERT: C 231 GLU cc_start: 0.6804 (mp0) cc_final: 0.6549 (mp0) REVERT: F 510 LYS cc_start: 0.8501 (ptpt) cc_final: 0.7132 (mmtt) REVERT: F 565 THR cc_start: 0.8808 (p) cc_final: 0.8426 (t) REVERT: F 578 GLU cc_start: 0.7418 (tt0) cc_final: 0.7168 (tt0) REVERT: F 597 TRP cc_start: 0.6321 (m-90) cc_final: 0.5864 (m100) outliers start: 52 outliers final: 36 residues processed: 282 average time/residue: 0.2772 time to fit residues: 110.3430 Evaluate side-chains 279 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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 103 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 577 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 0.0970 chunk 154 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115233 restraints weight = 21404.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112779 restraints weight = 53002.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.113557 restraints weight = 46963.156| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13821 Z= 0.140 Angle : 0.715 13.467 18834 Z= 0.335 Chirality : 0.047 0.393 2166 Planarity : 0.005 0.067 2337 Dihedral : 8.726 59.269 2667 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.89 % Favored : 96.81 % Rotamer: Outliers : 3.61 % Allowed : 14.21 % Favored : 82.18 % 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: -0.51 (0.21), residues: 1629 helix: 1.70 (0.39), residues: 180 sheet: -0.72 (0.19), residues: 675 loop : -0.31 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 36 HIS 0.004 0.001 HIS K 90 PHE 0.015 0.001 PHE J 72 TYR 0.020 0.002 TYR L 50 ARG 0.011 0.000 ARG E 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 15) link_NAG-ASN : angle 3.61233 ( 45) link_ALPHA1-6 : bond 0.01020 ( 6) link_ALPHA1-6 : angle 1.90527 ( 18) link_BETA1-4 : bond 0.01468 ( 15) link_BETA1-4 : angle 3.23334 ( 45) link_ALPHA1-3 : bond 0.01618 ( 6) link_ALPHA1-3 : angle 1.54382 ( 18) hydrogen bonds : bond 0.03477 ( 489) hydrogen bonds : angle 4.97020 ( 1251) SS BOND : bond 0.00152 ( 15) SS BOND : angle 0.76732 ( 30) covalent geometry : bond 0.00311 (13764) covalent geometry : angle 0.67292 (18678) *********************** 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 289 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 239 time to evaluate : 1.563 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: 0.6907 (OUTLIER) cc_final: 0.6118 (m-10) REVERT: G 33 LYS cc_start: 0.6040 (OUTLIER) cc_final: 0.5082 (mmtp) REVERT: G 54 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6960 (tt) REVERT: D 510 LYS cc_start: 0.8496 (ptpt) cc_final: 0.7206 (mmtt) REVERT: D 565 THR cc_start: 0.8606 (p) cc_final: 0.8295 (t) REVERT: D 597 TRP cc_start: 0.6467 (m-90) cc_final: 0.6047 (m100) REVERT: B 130 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7237 (mtm-85) REVERT: B 231 GLU cc_start: 0.7144 (mp0) cc_final: 0.6798 (mp0) REVERT: H 33 LYS cc_start: 0.5864 (OUTLIER) cc_final: 0.5130 (mttm) REVERT: K 48 LEU cc_start: 0.6501 (mp) cc_final: 0.6130 (mp) REVERT: K 92 TYR cc_start: 0.5469 (OUTLIER) cc_final: 0.5133 (m-80) REVERT: E 510 LYS cc_start: 0.8639 (ptpt) cc_final: 0.7323 (mmtt) REVERT: E 551 GLN cc_start: 0.8329 (tp40) cc_final: 0.7921 (tp40) REVERT: E 565 THR cc_start: 0.8696 (p) cc_final: 0.8435 (t) REVERT: E 597 TRP cc_start: 0.6370 (m-90) cc_final: 0.5979 (m100) REVERT: C 99 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.6312 (m-10) REVERT: C 184 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8795 (pp) REVERT: C 231 GLU cc_start: 0.6914 (mp0) cc_final: 0.6673 (mp0) REVERT: I 121 ASP cc_start: 0.7027 (t70) cc_final: 0.6614 (t70) REVERT: F 510 LYS cc_start: 0.8476 (ptpt) cc_final: 0.7083 (mmtt) REVERT: F 565 THR cc_start: 0.8768 (p) cc_final: 0.8399 (t) REVERT: F 578 GLU cc_start: 0.7452 (tt0) cc_final: 0.7213 (tt0) REVERT: F 597 TRP cc_start: 0.6345 (m-90) cc_final: 0.5860 (m100) outliers start: 50 outliers final: 37 residues processed: 275 average time/residue: 0.2850 time to fit residues: 110.2113 Evaluate side-chains 276 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 231 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 103 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 92 TYR Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 552 ASP 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 65 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 120 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118818 restraints weight = 21542.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117716 restraints weight = 55871.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114617 restraints weight = 39391.827| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13821 Z= 0.145 Angle : 0.709 11.288 18834 Z= 0.336 Chirality : 0.047 0.278 2166 Planarity : 0.005 0.069 2337 Dihedral : 8.500 59.527 2667 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.19 % Favored : 96.50 % Rotamer: Outliers : 3.46 % Allowed : 14.57 % Favored : 81.96 % 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: -0.46 (0.21), residues: 1629 helix: 1.71 (0.38), residues: 180 sheet: -0.71 (0.20), residues: 654 loop : -0.27 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP K 36 HIS 0.005 0.001 HIS F 549 PHE 0.023 0.001 PHE J 72 TYR 0.017 0.001 TYR H 100 ARG 0.010 0.001 ARG E 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 15) link_NAG-ASN : angle 2.89718 ( 45) link_ALPHA1-6 : bond 0.00954 ( 6) link_ALPHA1-6 : angle 1.74498 ( 18) link_BETA1-4 : bond 0.01491 ( 15) link_BETA1-4 : angle 3.28472 ( 45) link_ALPHA1-3 : bond 0.01637 ( 6) link_ALPHA1-3 : angle 1.63977 ( 18) hydrogen bonds : bond 0.03512 ( 489) hydrogen bonds : angle 4.96519 ( 1251) SS BOND : bond 0.00261 ( 15) SS BOND : angle 1.24435 ( 30) covalent geometry : bond 0.00326 (13764) covalent geometry : angle 0.67294 (18678) ********************** 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 284 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 1.528 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 99 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6120 (m-10) REVERT: G 33 LYS cc_start: 0.6006 (OUTLIER) cc_final: 0.5018 (mttm) REVERT: G 54 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.6905 (tt) REVERT: G 84 LEU cc_start: 0.6178 (pp) cc_final: 0.5800 (pt) REVERT: D 510 LYS cc_start: 0.8478 (ptpt) cc_final: 0.7180 (mmtt) REVERT: D 565 THR cc_start: 0.8668 (p) cc_final: 0.8337 (t) REVERT: D 597 TRP cc_start: 0.6457 (m-90) cc_final: 0.6063 (m100) REVERT: B 130 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7246 (mtm-85) REVERT: B 231 GLU cc_start: 0.7028 (mp0) cc_final: 0.6716 (mp0) REVERT: H 33 LYS cc_start: 0.5835 (OUTLIER) cc_final: 0.5035 (mttm) REVERT: K 48 LEU cc_start: 0.6365 (mp) cc_final: 0.5996 (mp) REVERT: K 92 TYR cc_start: 0.5323 (OUTLIER) cc_final: 0.5032 (m-80) REVERT: E 510 LYS cc_start: 0.8603 (ptpt) cc_final: 0.7231 (mmtt) REVERT: E 551 GLN cc_start: 0.8381 (tp40) cc_final: 0.7964 (tp40) REVERT: E 565 THR cc_start: 0.8797 (p) cc_final: 0.8530 (t) REVERT: E 597 TRP cc_start: 0.6367 (m-90) cc_final: 0.5951 (m100) REVERT: C 99 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6367 (m-10) REVERT: C 184 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8787 (pp) REVERT: C 231 GLU cc_start: 0.6955 (mp0) cc_final: 0.6635 (mp0) REVERT: I 54 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.6910 (tt) REVERT: I 121 ASP cc_start: 0.7020 (t70) cc_final: 0.6602 (t70) REVERT: F 510 LYS cc_start: 0.8466 (ptpt) cc_final: 0.7074 (mmtt) REVERT: F 565 THR cc_start: 0.8799 (p) cc_final: 0.8424 (t) REVERT: F 578 GLU cc_start: 0.7486 (tt0) cc_final: 0.7251 (tt0) REVERT: F 597 TRP cc_start: 0.6306 (m-90) cc_final: 0.5858 (m100) outliers start: 48 outliers final: 34 residues processed: 274 average time/residue: 0.2843 time to fit residues: 109.9391 Evaluate side-chains 270 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 103 GLU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain 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 227 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain 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 92 TYR Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 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 94 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 69 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 142 optimal weight: 0.4980 chunk 63 optimal weight: 0.0970 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 42 GLN J 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108595 restraints weight = 21508.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.106599 restraints weight = 52071.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107436 restraints weight = 47803.010| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13821 Z= 0.126 Angle : 0.708 15.173 18834 Z= 0.332 Chirality : 0.047 0.588 2166 Planarity : 0.005 0.074 2337 Dihedral : 7.625 59.912 2667 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.70 % Favored : 96.99 % Rotamer: Outliers : 2.81 % Allowed : 15.22 % Favored : 81.96 % 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: -0.42 (0.21), residues: 1629 helix: 1.85 (0.39), residues: 180 sheet: -0.82 (0.20), residues: 675 loop : -0.10 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP K 36 HIS 0.003 0.001 HIS D 549 PHE 0.032 0.001 PHE G 113 TYR 0.021 0.001 TYR L 50 ARG 0.011 0.000 ARG E 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 15) link_NAG-ASN : angle 3.70622 ( 45) link_ALPHA1-6 : bond 0.00870 ( 6) link_ALPHA1-6 : angle 1.64980 ( 18) link_BETA1-4 : bond 0.01511 ( 15) link_BETA1-4 : angle 3.29493 ( 45) link_ALPHA1-3 : bond 0.01648 ( 6) link_ALPHA1-3 : angle 1.76232 ( 18) hydrogen bonds : bond 0.03152 ( 489) hydrogen bonds : angle 4.89414 ( 1251) SS BOND : bond 0.00208 ( 15) SS BOND : angle 1.07746 ( 30) covalent geometry : bond 0.00271 (13764) covalent geometry : angle 0.66265 (18678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4225.54 seconds wall clock time: 74 minutes 17.68 seconds (4457.68 seconds total)