Starting phenix.real_space_refine on Thu Aug 6 22:39:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zv1_74844/08_2026/9zv1_74844.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zv1_74844/08_2026/9zv1_74844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zv1_74844/08_2026/9zv1_74844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zv1_74844/08_2026/9zv1_74844.map" model { file = "/net/cci-nas-00/data/ceres_data/9zv1_74844/08_2026/9zv1_74844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zv1_74844/08_2026/9zv1_74844.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 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 87 5.16 5 C 10901 2.51 5 N 2907 2.21 5 O 3405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17300 Number of models: 1 Model: "" Number of chains: 18 Chain: "H" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 929 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 822 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3864 Classifications: {'peptide': 484} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 20, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3865 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 20, 'TRANS': 463} Chain breaks: 1 Chain: "C" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3865 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 20, 'TRANS': 463} Chain breaks: 1 Chain: "I" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 929 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 822 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "D" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 929 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 822 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.94, per 1000 atoms: 0.17 Number of scatterers: 17300 At special positions: 0 Unit cell: (139.425, 150.975, 145.2, 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 87 16.00 O 3405 8.00 N 2907 7.00 C 10901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 498 " - pdb=" SG CYS A 502 " distance=2.04 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 491 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 77 " distance=1.96 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 498 " - pdb=" SG CYS B 502 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 491 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.00 Simple disulfide: pdb=" SG CYS C 302 " - pdb=" SG CYS C 326 " distance=2.02 Simple disulfide: pdb=" SG CYS C 498 " - pdb=" SG CYS C 502 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " BETA1-2 " MAN E 4 " - " NAG E 5 " " MAN F 4 " - " NAG F 5 " " MAN J 4 " - " NAG J 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG E 5 " - " GAL E 6 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG F 5 " - " GAL F 6 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG J 5 " - " GAL J 6 " BETA2-3 " GAL E 6 " - " SIA E 7 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL F 6 " - " SIA F 7 " " GAL J 6 " - " SIA J 7 " NAG-ASN " NAG A 601 " - " ASN A 310 " " NAG A 602 " - " ASN A 33 " " NAG A 603 " - " ASN A 508 " " NAG B 601 " - " ASN B 310 " " NAG B 602 " - " ASN B 33 " " NAG B 603 " - " ASN B 508 " " NAG C 601 " - " ASN C 310 " " NAG C 602 " - " ASN C 33 " " NAG C 603 " - " ASN C 508 " " NAG G 201 " - " ASN G 27A" " NAG K 201 " - " ASN K 27A" " NAG L 201 " - " ASN L 27A" Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 738.9 milliseconds 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3910 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 49 sheets defined 19.1% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.625A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.065A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 128 through 133 removed outlier: 3.983A pdb=" N TRP A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'A' and resid 391 through 412 Processing helix chain 'A' and resid 428 through 481 removed outlier: 3.574A pdb=" N GLN A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.670A pdb=" N VAL A 506 " --> pdb=" O CYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.551A pdb=" N SER A 517 " --> pdb=" O PRO A 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.981A pdb=" N TRP B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.529A pdb=" N THR B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 412 Processing helix chain 'B' and resid 428 through 481 removed outlier: 3.610A pdb=" N GLU B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 508 Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.894A pdb=" N SER B 517 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 128 through 133 removed outlier: 3.889A pdb=" N TRP C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 205 Processing helix chain 'C' and resid 391 through 412 Processing helix chain 'C' and resid 428 through 481 removed outlier: 3.521A pdb=" N GLU C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 509 removed outlier: 3.871A pdb=" N SER C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 517 Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.625A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.065A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.625A pdb=" N THR D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.064A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.524A pdb=" N LEU H 18 " --> pdb=" O TRP H 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.719A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.563A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.784A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 13 through 17 removed outlier: 3.529A pdb=" N CYS A 14 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 377 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.784A pdb=" N THR A 28 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LYS A 32 " --> pdb=" O THR A 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA9, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB1, first strand: chain 'A' and resid 51 through 53 removed outlier: 7.297A pdb=" N LEU A 51 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N CYS A 298 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.593A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.509A pdb=" N SER A 104 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N TRP A 244 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 185 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU A 189 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR A 266 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.509A pdb=" N SER A 104 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N TRP A 244 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LEU A 189 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'A' and resid 143 through 148 removed outlier: 4.491A pdb=" N CYS A 146 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 174 through 176 Processing sheet with id=AB8, first strand: chain 'A' and resid 302 through 304 removed outlier: 4.848A pdb=" N CYS A 302 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 13 through 17 removed outlier: 3.512A pdb=" N CYS B 14 " --> pdb=" O HIS B 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC2, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'B' and resid 51 through 54 removed outlier: 7.149A pdb=" N LEU B 51 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N CYS B 298 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.392A pdb=" N LEU B 60 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.560A pdb=" N SER B 104 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N TRP B 244 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU B 189 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR B 266 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.560A pdb=" N SER B 104 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N TRP B 244 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU B 189 " --> pdb=" O PRO B 264 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 143 through 148 removed outlier: 4.534A pdb=" N CYS B 146 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 174 through 179 Processing sheet with id=AD1, first strand: chain 'B' and resid 307 through 309 removed outlier: 4.102A pdb=" N CYS B 302 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 13 through 17 removed outlier: 3.629A pdb=" N CYS C 14 " --> pdb=" O HIS C 379 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN C 382 " --> pdb=" O GLY C 385 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY C 385 " --> pdb=" O ASN C 382 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD4, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD5, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.170A pdb=" N ASP C 53 " --> pdb=" O THR C 300 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 60 through 63 removed outlier: 6.296A pdb=" N VAL C 90 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE C 89 " --> pdb=" O MET C 289 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.545A pdb=" N SER C 104 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N TRP C 244 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP C 185 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU C 189 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR C 266 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.545A pdb=" N SER C 104 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N TRP C 244 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU C 189 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AE1, first strand: chain 'C' and resid 143 through 148 removed outlier: 7.710A pdb=" N ALA C 145 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N ALA C 152 " --> pdb=" O ALA C 145 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 174 through 179 Processing sheet with id=AE3, first strand: chain 'C' and resid 302 through 303 removed outlier: 3.647A pdb=" N GLU C 418 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.525A pdb=" N LEU I 18 " --> pdb=" O TRP I 82 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.719A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 5 through 7 Processing sheet with id=AE7, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.562A pdb=" N VAL K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.784A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.524A pdb=" N LEU D 18 " --> pdb=" O TRP D 82 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.720A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AF3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.562A pdb=" N VAL G 85 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.784A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1791 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: 3.88 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2866 1.31 - 1.44: 5008 1.44 - 1.58: 9705 1.58 - 1.71: 0 1.71 - 1.85: 126 Bond restraints: 17705 Sorted by residual: bond pdb=" C PRO C 84 " pdb=" O PRO C 84 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.23e-02 6.61e+03 2.54e+01 bond pdb=" C PRO B 84 " pdb=" O PRO B 84 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.30e-02 5.92e+03 1.85e+01 bond pdb=" N ASN C 508 " pdb=" CA ASN C 508 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.23e-02 6.61e+03 1.63e+01 bond pdb=" C MET C 76 " pdb=" N CYS C 77 " ideal model delta sigma weight residual 1.331 1.285 0.046 1.25e-02 6.40e+03 1.37e+01 bond pdb=" C PRO C 75 " pdb=" O PRO C 75 " ideal model delta sigma weight residual 1.236 1.188 0.049 1.36e-02 5.41e+03 1.28e+01 ... (remaining 17700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 23454 2.97 - 5.94: 485 5.94 - 8.91: 42 8.91 - 11.88: 20 11.88 - 14.85: 3 Bond angle restraints: 24004 Sorted by residual: angle pdb=" CA ASN C 508 " pdb=" CB ASN C 508 " pdb=" CG ASN C 508 " ideal model delta sigma weight residual 112.60 124.45 -11.85 1.00e+00 1.00e+00 1.40e+02 angle pdb=" N ASN C 508 " pdb=" CA ASN C 508 " pdb=" CB ASN C 508 " ideal model delta sigma weight residual 110.06 121.92 -11.86 1.50e+00 4.44e-01 6.25e+01 angle pdb=" N VAL B 83 " pdb=" CA VAL B 83 " pdb=" C VAL B 83 " ideal model delta sigma weight residual 109.19 102.82 6.37 8.20e-01 1.49e+00 6.03e+01 angle pdb=" N CYS C 77 " pdb=" CA CYS C 77 " pdb=" CB CYS C 77 " ideal model delta sigma weight residual 111.52 97.83 13.69 1.86e+00 2.89e-01 5.41e+01 angle pdb=" C MET B 76 " pdb=" N CYS B 77 " pdb=" CA CYS B 77 " ideal model delta sigma weight residual 122.58 107.73 14.85 2.07e+00 2.33e-01 5.15e+01 ... (remaining 23999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.88: 9952 22.88 - 45.76: 796 45.76 - 68.64: 178 68.64 - 91.51: 26 91.51 - 114.39: 29 Dihedral angle restraints: 10981 sinusoidal: 4845 harmonic: 6136 Sorted by residual: dihedral pdb=" C CYS B 77 " pdb=" N CYS B 77 " pdb=" CA CYS B 77 " pdb=" CB CYS B 77 " ideal model delta harmonic sigma weight residual -122.60 -142.13 19.53 0 2.50e+00 1.60e-01 6.10e+01 dihedral pdb=" CB CYS C 498 " pdb=" SG CYS C 498 " pdb=" SG CYS C 502 " pdb=" CB CYS C 502 " ideal model delta sinusoidal sigma weight residual 93.00 158.27 -65.27 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS B 52 " pdb=" SG CYS B 52 " pdb=" SG CYS B 298 " pdb=" CB CYS B 298 " ideal model delta sinusoidal sigma weight residual -86.00 -24.85 -61.15 1 1.00e+01 1.00e-02 4.97e+01 ... (remaining 10978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.895: 2656 0.895 - 1.791: 0 1.791 - 2.686: 0 2.686 - 3.582: 0 3.582 - 4.477: 1 Chirality restraints: 2657 Sorted by residual: chirality pdb=" C2 SIA F 7 " pdb=" O3 GAL F 6 " pdb=" C1 SIA F 7 " pdb=" O6 SIA F 7 " both_signs ideal model delta sigma weight residual False -2.50 -3.02 0.52 2.00e-02 2.50e+03 6.64e+02 chirality pdb=" C2 SIA E 7 " pdb=" O3 GAL E 6 " pdb=" C1 SIA E 7 " pdb=" O6 SIA E 7 " both_signs ideal model delta sigma weight residual False -2.50 -3.01 0.51 2.00e-02 2.50e+03 6.51e+02 chirality pdb=" C2 SIA J 7 " pdb=" O3 GAL J 6 " pdb=" C1 SIA J 7 " pdb=" O6 SIA J 7 " both_signs ideal model delta sigma weight residual False -2.50 -3.00 0.50 2.00e-02 2.50e+03 6.34e+02 ... (remaining 2654 not shown) Planarity restraints: 3081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 603 " -0.328 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C7 NAG A 603 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG A 603 " -0.117 2.00e-02 2.50e+03 pdb=" N2 NAG A 603 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG A 603 " -0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 201 " -0.307 2.00e-02 2.50e+03 2.66e-01 8.86e+02 pdb=" C7 NAG G 201 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG G 201 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG G 201 " 0.473 2.00e-02 2.50e+03 pdb=" O7 NAG G 201 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 201 " -0.304 2.00e-02 2.50e+03 2.64e-01 8.71e+02 pdb=" C7 NAG K 201 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG K 201 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG K 201 " 0.469 2.00e-02 2.50e+03 pdb=" O7 NAG K 201 " -0.085 2.00e-02 2.50e+03 ... (remaining 3078 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 23 2.56 - 3.14: 12592 3.14 - 3.73: 26169 3.73 - 4.31: 39828 4.31 - 4.90: 65358 Nonbonded interactions: 143970 Sorted by model distance: nonbonded pdb=" NZ LYS B 58 " pdb=" OD1 ASP D 96 " model vdw 1.972 3.120 nonbonded pdb=" OD1 ASP H 96 " pdb=" NZ LYS C 58 " model vdw 2.055 3.120 nonbonded pdb=" OD2 ASP B 78 " pdb=" OG SER D 100 " model vdw 2.261 3.040 nonbonded pdb=" O MET B 76 " pdb=" CA CYS B 77 " model vdw 2.307 2.776 nonbonded pdb=" OD2 ASP H 96 " pdb=" NZ LYS C 58 " model vdw 2.367 3.120 ... (remaining 143965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 11 through 251 or (resid 252 and (name N or name CA or nam \ e C or name O )) or resid 253 through 603)) selection = (chain 'C' and (resid 11 through 251 or (resid 252 and (name N or name CA or nam \ e C or name O )) or resid 253 through 603)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' } 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 individual isotropic 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: 4.270 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.660 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 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 : 0.005 0.073 17756 Z= 0.300 Angle : 1.055 17.312 24136 Z= 0.588 Chirality : 0.108 4.477 2657 Planarity : 0.015 0.285 3069 Dihedral : 17.882 114.394 7008 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.40 % Favored : 92.84 % Rotamer: Outliers : 2.33 % Allowed : 22.31 % Favored : 75.35 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.18), residues: 2109 helix: -0.04 (0.27), residues: 330 sheet: -0.74 (0.23), residues: 546 loop : -1.61 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 54 TYR 0.030 0.002 TYR C 516 PHE 0.028 0.002 PHE A 494 TRP 0.022 0.001 TRP C 86 HIS 0.024 0.002 HIS B 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.30 (17705) covalent geometry : angle 0.99311 / 0.58 (24004) SS BOND : bond 0.01761 / 0.98 ( 21) SS BOND : angle 3.37384 / 2.62 ( 42) hydrogen bonds : bond 0.20489 / 13.14 ( 629) hydrogen bonds : angle 8.37964 / 5.71 ( 1791) link_ALPHA1-3 : bond 0.00554 / 0.24 ( 3) link_ALPHA1-3 : angle 2.25889 / 1.17 ( 9) link_BETA1-2 : bond 0.00458 / 0.21 ( 3) link_BETA1-2 : angle 2.32796 / 1.36 ( 9) link_BETA1-4 : bond 0.00464 / 0.31 ( 9) link_BETA1-4 : angle 4.18720 / 2.67 ( 27) link_BETA2-3 : bond 0.06929 / 3.22 ( 3) link_BETA2-3 : angle 11.46215 / 6.00 ( 9) link_NAG-ASN : bond 0.01222 / 0.85 ( 12) link_NAG-ASN : angle 5.17368 / 3.50 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7167 (mt-10) REVERT: A 30 MET cc_start: 0.8157 (mtm) cc_final: 0.7765 (mtt) REVERT: A 31 GLU cc_start: 0.6884 (tt0) cc_final: 0.5955 (mt-10) REVERT: A 50 LYS cc_start: 0.6668 (mttm) cc_final: 0.6167 (mttt) REVERT: A 175 LYS cc_start: 0.7358 (mttt) cc_final: 0.6300 (mmmt) REVERT: A 196 ASN cc_start: 0.6840 (p0) cc_final: 0.4167 (t0) REVERT: A 285 ASP cc_start: 0.5383 (OUTLIER) cc_final: 0.4621 (p0) REVERT: A 290 LYS cc_start: 0.7282 (mmtm) cc_final: 0.7075 (mmtt) REVERT: A 294 GLU cc_start: 0.6031 (mp0) cc_final: 0.5830 (mp0) REVERT: A 309 ILE cc_start: 0.6135 (OUTLIER) cc_final: 0.5909 (mm) REVERT: A 331 LYS cc_start: 0.7776 (tttp) cc_final: 0.6982 (tttt) REVERT: A 341 LEU cc_start: 0.8103 (mp) cc_final: 0.7874 (mp) REVERT: A 397 LYS cc_start: 0.6904 (ttmm) cc_final: 0.6643 (mttp) REVERT: A 404 ASN cc_start: 0.6626 (m-40) cc_final: 0.6231 (t0) REVERT: A 456 MET cc_start: 0.6734 (mtp) cc_final: 0.6333 (mtm) REVERT: A 459 GLU cc_start: 0.6766 (tt0) cc_final: 0.5841 (tp30) REVERT: A 460 ARG cc_start: 0.6961 (mmm-85) cc_final: 0.6356 (mtp180) REVERT: A 470 LYS cc_start: 0.7160 (tttp) cc_final: 0.6771 (mtpp) REVERT: A 475 LYS cc_start: 0.7415 (mtpp) cc_final: 0.6962 (ttmt) REVERT: A 485 LYS cc_start: 0.7307 (tttt) cc_final: 0.6648 (ttpp) REVERT: B 30 MET cc_start: 0.7193 (mmt) cc_final: 0.6950 (mmt) REVERT: B 32 LYS cc_start: 0.7900 (mttt) cc_final: 0.6532 (mmtt) REVERT: B 63 LYS cc_start: 0.6257 (mttt) cc_final: 0.5926 (mttp) REVERT: B 175 LYS cc_start: 0.7509 (mtpp) cc_final: 0.6510 (mmmt) REVERT: B 176 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6658 (pt) REVERT: B 196 ASN cc_start: 0.6640 (p0) cc_final: 0.3913 (t0) REVERT: B 203 ASN cc_start: 0.6700 (m-40) cc_final: 0.6372 (m-40) REVERT: B 256 GLU cc_start: 0.7376 (tt0) cc_final: 0.7103 (tt0) REVERT: B 325 GLU cc_start: 0.6462 (mp0) cc_final: 0.6111 (mp0) REVERT: B 334 LYS cc_start: 0.6284 (mtmm) cc_final: 0.5901 (pttp) REVERT: B 432 GLU cc_start: 0.7227 (tt0) cc_final: 0.7015 (tt0) REVERT: B 444 ASP cc_start: 0.7887 (m-30) cc_final: 0.7635 (m-30) REVERT: B 459 GLU cc_start: 0.6900 (tt0) cc_final: 0.5808 (tp30) REVERT: B 460 ARG cc_start: 0.6657 (mtp180) cc_final: 0.6181 (mtt180) REVERT: B 470 LYS cc_start: 0.6861 (tttm) cc_final: 0.6376 (ttpt) REVERT: B 475 LYS cc_start: 0.6975 (ttpt) cc_final: 0.6609 (ttmt) REVERT: B 485 LYS cc_start: 0.7594 (ttpp) cc_final: 0.7235 (tttp) REVERT: C 31 GLU cc_start: 0.6910 (tt0) cc_final: 0.5825 (mt-10) REVERT: C 50 LYS cc_start: 0.6782 (mttp) cc_final: 0.6324 (mttt) REVERT: C 76 MET cc_start: 0.7104 (mtp) cc_final: 0.6894 (mtp) REVERT: C 79 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.6172 (tt0) REVERT: C 175 LYS cc_start: 0.7419 (mttt) cc_final: 0.6213 (mmmt) REVERT: C 196 ASN cc_start: 0.6798 (p0) cc_final: 0.3836 (t0) REVERT: C 290 LYS cc_start: 0.7392 (mmtm) cc_final: 0.7107 (mmtt) REVERT: C 294 GLU cc_start: 0.7059 (pm20) cc_final: 0.6267 (pm20) REVERT: C 330 VAL cc_start: 0.6513 (OUTLIER) cc_final: 0.6159 (t) REVERT: C 392 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6628 (mmpt) REVERT: C 426 ASN cc_start: 0.7112 (t0) cc_final: 0.6899 (t0) REVERT: C 432 GLU cc_start: 0.6976 (tt0) cc_final: 0.6670 (tt0) REVERT: C 436 LYS cc_start: 0.7092 (ttpp) cc_final: 0.6867 (ptmt) REVERT: C 456 MET cc_start: 0.6565 (ttm) cc_final: 0.5984 (mtp) REVERT: C 466 ASP cc_start: 0.7385 (t0) cc_final: 0.7099 (m-30) REVERT: C 467 SER cc_start: 0.7593 (OUTLIER) cc_final: 0.7375 (p) REVERT: C 470 LYS cc_start: 0.6625 (tttp) cc_final: 0.6403 (tptm) REVERT: C 475 LYS cc_start: 0.6757 (mtpp) cc_final: 0.6255 (mtmt) REVERT: G 50 ASP cc_start: 0.7495 (t0) cc_final: 0.7129 (t70) outliers start: 43 outliers final: 14 residues processed: 324 average time/residue: 0.5647 time to fit residues: 204.1567 Evaluate side-chains 260 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain G residue 21 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 31 ASN H 39 GLN A 48 ASN A 380 HIS A 416 GLN B 48 ASN B 254 HIS B 384 GLN B 425 ASN C 254 HIS I 39 GLN D 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.161502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.128448 restraints weight = 17657.119| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.08 r_work: 0.3267 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17756 Z= 0.239 Angle : 0.806 14.562 24136 Z= 0.396 Chirality : 0.053 0.391 2657 Planarity : 0.006 0.067 3069 Dihedral : 11.786 83.570 3052 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.97 % Favored : 93.50 % Rotamer: Outliers : 5.27 % Allowed : 18.08 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.17), residues: 2109 helix: 0.80 (0.26), residues: 351 sheet: -0.34 (0.23), residues: 540 loop : -1.66 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 92 TYR 0.015 0.002 TYR K 32 PHE 0.024 0.002 PHE C 424 TRP 0.011 0.002 TRP C 375 HIS 0.012 0.002 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (17705) covalent geometry : angle 0.76125 / 0.39 (24004) SS BOND : bond 0.00444 / 0.29 ( 21) SS BOND : angle 2.45616 / 1.44 ( 42) hydrogen bonds : bond 0.05028 / 3.27 ( 629) hydrogen bonds : angle 5.86708 / 4.05 ( 1791) link_ALPHA1-3 : bond 0.00936 / 0.44 ( 3) link_ALPHA1-3 : angle 2.82359 / 1.62 ( 9) link_BETA1-2 : bond 0.00513 / 0.24 ( 3) link_BETA1-2 : angle 1.57867 / 0.90 ( 9) link_BETA1-4 : bond 0.00304 / 0.18 ( 9) link_BETA1-4 : angle 3.06887 / 1.91 ( 27) link_BETA2-3 : bond 0.00974 / 0.43 ( 3) link_BETA2-3 : angle 6.60430 / 3.45 ( 9) link_NAG-ASN : bond 0.01073 / 0.53 ( 12) link_NAG-ASN : angle 4.62069 / 3.09 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 229 time to evaluate : 0.703 Fit side-chains REVERT: H 3 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8137 (pt0) REVERT: H 66 GLN cc_start: 0.8004 (mt0) cc_final: 0.7725 (mt0) REVERT: H 81 GLN cc_start: 0.8051 (tt0) cc_final: 0.7613 (tt0) REVERT: L 27 GLN cc_start: 0.8175 (pt0) cc_final: 0.7973 (pt0) REVERT: L 50 ASP cc_start: 0.8130 (t0) cc_final: 0.7542 (t0) REVERT: A 31 GLU cc_start: 0.8159 (tt0) cc_final: 0.7671 (mt-10) REVERT: A 50 LYS cc_start: 0.8371 (mttm) cc_final: 0.8037 (mttm) REVERT: A 64 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8389 (m-30) REVERT: A 175 LYS cc_start: 0.8724 (mttt) cc_final: 0.8036 (tptp) REVERT: A 196 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.5602 (t0) REVERT: A 331 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8046 (tttt) REVERT: A 459 GLU cc_start: 0.8087 (tt0) cc_final: 0.7780 (tp30) REVERT: A 460 ARG cc_start: 0.8148 (mmm-85) cc_final: 0.7843 (mtp180) REVERT: A 470 LYS cc_start: 0.8002 (tttp) cc_final: 0.7771 (mtpp) REVERT: A 475 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7700 (ttmt) REVERT: A 485 LYS cc_start: 0.7719 (tttt) cc_final: 0.7201 (ttpp) REVERT: A 497 LYS cc_start: 0.5319 (OUTLIER) cc_final: 0.5066 (tmtt) REVERT: B 32 LYS cc_start: 0.8652 (mttt) cc_final: 0.7710 (mmtt) REVERT: B 79 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7033 (tt0) REVERT: B 175 LYS cc_start: 0.8770 (mtpp) cc_final: 0.7867 (tptp) REVERT: B 237 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8398 (mtt-85) REVERT: B 325 GLU cc_start: 0.7734 (mp0) cc_final: 0.7448 (mp0) REVERT: B 334 LYS cc_start: 0.8034 (mtmm) cc_final: 0.7749 (mtmt) REVERT: B 432 GLU cc_start: 0.8688 (tt0) cc_final: 0.8464 (tt0) REVERT: B 459 GLU cc_start: 0.8064 (tt0) cc_final: 0.7557 (tp30) REVERT: B 460 ARG cc_start: 0.7893 (mtp180) cc_final: 0.7610 (mtt180) REVERT: C 50 LYS cc_start: 0.8566 (mttp) cc_final: 0.8349 (mttt) REVERT: C 79 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: C 175 LYS cc_start: 0.8760 (mttt) cc_final: 0.7951 (tptp) REVERT: C 196 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.7954 (p0) REVERT: C 294 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: C 432 GLU cc_start: 0.8736 (tt0) cc_final: 0.8485 (tt0) REVERT: C 449 ASN cc_start: 0.8872 (m-40) cc_final: 0.8590 (m110) REVERT: C 466 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8361 (OUTLIER) REVERT: C 475 LYS cc_start: 0.7716 (mtpp) cc_final: 0.7248 (mtmt) REVERT: C 504 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.5608 (tm-30) REVERT: I 3 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7850 (pt0) REVERT: I 58 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8045 (ttm-80) REVERT: I 66 GLN cc_start: 0.8009 (mt0) cc_final: 0.7754 (mt0) REVERT: K 50 ASP cc_start: 0.8197 (t0) cc_final: 0.7835 (t70) REVERT: D 3 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: D 66 GLN cc_start: 0.8082 (mt0) cc_final: 0.7763 (mt0) REVERT: G 4 LEU cc_start: 0.8175 (mt) cc_final: 0.7832 (tt) REVERT: G 50 ASP cc_start: 0.8136 (t0) cc_final: 0.7764 (t70) outliers start: 97 outliers final: 29 residues processed: 303 average time/residue: 0.5734 time to fit residues: 193.5376 Evaluate side-chains 253 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 211 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 61 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 153 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN A 380 HIS C 414 ASN C 426 ASN I 39 GLN D 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.154318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.121345 restraints weight = 18188.500| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.06 r_work: 0.3153 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17756 Z= 0.171 Angle : 0.692 12.442 24136 Z= 0.341 Chirality : 0.049 0.382 2657 Planarity : 0.005 0.049 3069 Dihedral : 10.025 82.384 3033 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.36 % Favored : 94.17 % Rotamer: Outliers : 4.56 % Allowed : 19.22 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.18), residues: 2109 helix: 1.70 (0.26), residues: 333 sheet: -0.09 (0.25), residues: 489 loop : -1.55 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 92 TYR 0.013 0.002 TYR C 178 PHE 0.015 0.002 PHE B 156 TRP 0.007 0.001 TRP D 82 HIS 0.012 0.001 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (17705) covalent geometry : angle 0.65164 / 0.33 (24004) SS BOND : bond 0.00555 / 0.26 ( 21) SS BOND : angle 2.06731 / 1.23 ( 42) hydrogen bonds : bond 0.04367 / 2.83 ( 629) hydrogen bonds : angle 5.43112 / 3.75 ( 1791) link_ALPHA1-3 : bond 0.01169 / 0.54 ( 3) link_ALPHA1-3 : angle 1.81635 / 1.04 ( 9) link_BETA1-2 : bond 0.00249 / 0.12 ( 3) link_BETA1-2 : angle 1.19135 / 0.67 ( 9) link_BETA1-4 : bond 0.00310 / 0.21 ( 9) link_BETA1-4 : angle 2.87432 / 1.75 ( 27) link_BETA2-3 : bond 0.00716 / 0.34 ( 3) link_BETA2-3 : angle 6.21363 / 3.29 ( 9) link_NAG-ASN : bond 0.00663 / 0.39 ( 12) link_NAG-ASN : angle 3.98922 / 2.68 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 221 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8003 (pt0) REVERT: H 23 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: H 58 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7567 (tpp-160) REVERT: H 66 GLN cc_start: 0.8037 (mt0) cc_final: 0.7704 (mt0) REVERT: H 68 THR cc_start: 0.8641 (m) cc_final: 0.8426 (m) REVERT: L 27 GLN cc_start: 0.8162 (pt0) cc_final: 0.7947 (pt0) REVERT: L 50 ASP cc_start: 0.8071 (t0) cc_final: 0.7463 (t0) REVERT: A 31 GLU cc_start: 0.8016 (tt0) cc_final: 0.7377 (mt-10) REVERT: A 50 LYS cc_start: 0.8325 (mttm) cc_final: 0.7995 (mttp) REVERT: A 175 LYS cc_start: 0.8724 (mttt) cc_final: 0.8006 (tptp) REVERT: A 196 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.5414 (t0) REVERT: A 290 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.7513 (mmtt) REVERT: A 294 GLU cc_start: 0.7508 (mp0) cc_final: 0.7256 (mp0) REVERT: A 331 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7819 (tttt) REVERT: A 341 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8570 (mp) REVERT: A 459 GLU cc_start: 0.8031 (tt0) cc_final: 0.7643 (tp30) REVERT: A 460 ARG cc_start: 0.8040 (mmm-85) cc_final: 0.7674 (mtp180) REVERT: A 467 SER cc_start: 0.8517 (p) cc_final: 0.8294 (p) REVERT: A 470 LYS cc_start: 0.7881 (tttp) cc_final: 0.7508 (tptt) REVERT: A 475 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7546 (ttmt) REVERT: A 485 LYS cc_start: 0.7606 (tttt) cc_final: 0.7035 (ttpp) REVERT: B 31 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7935 (mp0) REVERT: B 32 LYS cc_start: 0.8614 (mttt) cc_final: 0.7634 (mmtt) REVERT: B 175 LYS cc_start: 0.8713 (mtpp) cc_final: 0.7871 (tptp) REVERT: B 183 ARG cc_start: 0.7459 (mmp-170) cc_final: 0.6940 (mmp80) REVERT: B 199 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: B 325 GLU cc_start: 0.7661 (mp0) cc_final: 0.7312 (mp0) REVERT: B 432 GLU cc_start: 0.8572 (tt0) cc_final: 0.8367 (tt0) REVERT: B 459 GLU cc_start: 0.8063 (tt0) cc_final: 0.7446 (tp30) REVERT: B 460 ARG cc_start: 0.7824 (mtp180) cc_final: 0.7516 (mtt180) REVERT: B 470 LYS cc_start: 0.7750 (tptm) cc_final: 0.7402 (tptt) REVERT: B 485 LYS cc_start: 0.7851 (ttpp) cc_final: 0.7612 (tttp) REVERT: C 175 LYS cc_start: 0.8771 (mttt) cc_final: 0.7883 (tptp) REVERT: C 294 GLU cc_start: 0.8206 (pm20) cc_final: 0.7760 (pm20) REVERT: C 321 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8320 (mt) REVERT: C 432 GLU cc_start: 0.8642 (tt0) cc_final: 0.8361 (tt0) REVERT: C 449 ASN cc_start: 0.8788 (m-40) cc_final: 0.8576 (m110) REVERT: C 466 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8289 (OUTLIER) REVERT: C 475 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7192 (mtmt) REVERT: C 504 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.5907 (mp0) REVERT: I 58 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8130 (ttm-80) REVERT: I 66 GLN cc_start: 0.8024 (mt0) cc_final: 0.7671 (mt0) REVERT: K 24 ARG cc_start: 0.8018 (mtp180) cc_final: 0.7716 (mtp180) REVERT: K 50 ASP cc_start: 0.8181 (t0) cc_final: 0.7679 (t70) REVERT: D 23 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: D 66 GLN cc_start: 0.8134 (mt0) cc_final: 0.7703 (mt0) REVERT: G 4 LEU cc_start: 0.8040 (mt) cc_final: 0.7681 (tt) REVERT: G 24 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7885 (mtp85) REVERT: G 50 ASP cc_start: 0.8050 (t0) cc_final: 0.7668 (t70) outliers start: 84 outliers final: 35 residues processed: 281 average time/residue: 0.5475 time to fit residues: 171.8507 Evaluate side-chains 261 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 475 LYS Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain D residue 23 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 194 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 152 optimal weight: 8.9990 chunk 173 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN A 47 HIS A 48 ASN C 343 ASN C 425 ASN C 426 ASN I 39 GLN D 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.152798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119550 restraints weight = 18158.367| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.04 r_work: 0.3135 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17756 Z= 0.188 Angle : 0.700 12.063 24136 Z= 0.344 Chirality : 0.050 0.483 2657 Planarity : 0.005 0.050 3069 Dihedral : 8.930 80.695 3027 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.74 % Favored : 93.84 % Rotamer: Outliers : 4.51 % Allowed : 19.98 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.18), residues: 2109 helix: 1.90 (0.27), residues: 333 sheet: -0.09 (0.24), residues: 483 loop : -1.51 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 117 TYR 0.013 0.002 TYR C 178 PHE 0.016 0.002 PHE C 156 TRP 0.008 0.001 TRP D 82 HIS 0.015 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (17705) covalent geometry : angle 0.66097 / 0.33 (24004) SS BOND : bond 0.00376 / 0.25 ( 21) SS BOND : angle 2.02807 / 1.18 ( 42) hydrogen bonds : bond 0.04291 / 2.81 ( 629) hydrogen bonds : angle 5.36207 / 3.71 ( 1791) link_ALPHA1-3 : bond 0.00932 / 0.42 ( 3) link_ALPHA1-3 : angle 2.35648 / 1.35 ( 9) link_BETA1-2 : bond 0.00229 / 0.11 ( 3) link_BETA1-2 : angle 1.21241 / 0.70 ( 9) link_BETA1-4 : bond 0.00397 / 0.29 ( 9) link_BETA1-4 : angle 2.87689 / 1.75 ( 27) link_BETA2-3 : bond 0.00669 / 0.31 ( 3) link_BETA2-3 : angle 6.39520 / 3.39 ( 9) link_NAG-ASN : bond 0.00736 / 0.37 ( 12) link_NAG-ASN : angle 3.83047 / 2.54 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 219 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: H 23 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: H 58 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7510 (tpp-160) REVERT: H 66 GLN cc_start: 0.8092 (mt0) cc_final: 0.7754 (mt0) REVERT: H 68 THR cc_start: 0.8601 (m) cc_final: 0.8383 (m) REVERT: H 81 GLN cc_start: 0.7962 (tt0) cc_final: 0.7505 (tt0) REVERT: L 50 ASP cc_start: 0.8054 (t0) cc_final: 0.7438 (t70) REVERT: A 31 GLU cc_start: 0.8078 (tt0) cc_final: 0.7405 (mt-10) REVERT: A 50 LYS cc_start: 0.8301 (mttm) cc_final: 0.7954 (mttp) REVERT: A 175 LYS cc_start: 0.8720 (mttt) cc_final: 0.8009 (tptp) REVERT: A 196 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.7799 (p0) REVERT: A 294 GLU cc_start: 0.7575 (mp0) cc_final: 0.7303 (mp0) REVERT: A 301 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7837 (ttpt) REVERT: A 331 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7757 (tttt) REVERT: A 459 GLU cc_start: 0.8064 (tt0) cc_final: 0.7642 (tp30) REVERT: A 460 ARG cc_start: 0.8030 (mmm-85) cc_final: 0.7662 (mtp180) REVERT: A 467 SER cc_start: 0.8505 (p) cc_final: 0.8281 (p) REVERT: A 470 LYS cc_start: 0.7942 (tttp) cc_final: 0.7487 (tptp) REVERT: A 475 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7511 (ttmt) REVERT: A 485 LYS cc_start: 0.7651 (tttt) cc_final: 0.7090 (ttpp) REVERT: B 27 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7788 (m-30) REVERT: B 31 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7981 (mp0) REVERT: B 32 LYS cc_start: 0.8606 (mttt) cc_final: 0.7679 (mmtt) REVERT: B 175 LYS cc_start: 0.8721 (mtpp) cc_final: 0.7853 (tptp) REVERT: B 183 ARG cc_start: 0.7455 (mmp-170) cc_final: 0.6960 (mmp80) REVERT: B 199 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: B 459 GLU cc_start: 0.8146 (tt0) cc_final: 0.7569 (tp30) REVERT: B 460 ARG cc_start: 0.7793 (mtp180) cc_final: 0.7501 (mtt180) REVERT: C 175 LYS cc_start: 0.8801 (mttt) cc_final: 0.7922 (tptp) REVERT: C 237 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8404 (mtt-85) REVERT: C 294 GLU cc_start: 0.8193 (pm20) cc_final: 0.7822 (pm20) REVERT: C 321 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8330 (mt) REVERT: C 432 GLU cc_start: 0.8679 (tt0) cc_final: 0.8399 (tt0) REVERT: C 466 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8339 (OUTLIER) REVERT: C 475 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7248 (mtmt) REVERT: C 504 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.5810 (mp0) REVERT: I 3 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7667 (pt0) REVERT: I 43 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7713 (mmtm) REVERT: I 58 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8133 (ttm-80) REVERT: I 66 GLN cc_start: 0.8089 (mt0) cc_final: 0.7751 (mt0) REVERT: K 24 ARG cc_start: 0.8018 (mtp180) cc_final: 0.7686 (mtp180) REVERT: K 50 ASP cc_start: 0.8190 (t0) cc_final: 0.7638 (t70) REVERT: D 23 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: D 66 GLN cc_start: 0.8165 (mt0) cc_final: 0.7844 (mt0) REVERT: G 4 LEU cc_start: 0.8032 (mt) cc_final: 0.7695 (tt) REVERT: G 24 ARG cc_start: 0.8145 (mtp180) cc_final: 0.7250 (mtp180) outliers start: 83 outliers final: 42 residues processed: 276 average time/residue: 0.5348 time to fit residues: 164.7945 Evaluate side-chains 265 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 475 LYS Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 64 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 153 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 GLN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN D 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.153195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.120171 restraints weight = 18050.588| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.03 r_work: 0.3145 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17756 Z= 0.171 Angle : 0.685 15.706 24136 Z= 0.334 Chirality : 0.050 0.689 2657 Planarity : 0.005 0.049 3069 Dihedral : 8.557 81.532 3027 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.74 % Favored : 93.84 % Rotamer: Outliers : 4.78 % Allowed : 20.03 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 2109 helix: 1.98 (0.27), residues: 333 sheet: -0.03 (0.24), residues: 489 loop : -1.50 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 507 TYR 0.012 0.001 TYR C 178 PHE 0.015 0.002 PHE B 156 TRP 0.009 0.001 TRP D 82 HIS 0.010 0.001 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (17705) covalent geometry : angle 0.63607 / 0.32 (24004) SS BOND : bond 0.00375 / 0.24 ( 21) SS BOND : angle 1.96074 / 1.16 ( 42) hydrogen bonds : bond 0.04102 / 2.67 ( 629) hydrogen bonds : angle 5.24914 / 3.63 ( 1791) link_ALPHA1-3 : bond 0.00977 / 0.44 ( 3) link_ALPHA1-3 : angle 2.12609 / 1.22 ( 9) link_BETA1-2 : bond 0.00251 / 0.11 ( 3) link_BETA1-2 : angle 1.10185 / 0.63 ( 9) link_BETA1-4 : bond 0.00398 / 0.28 ( 9) link_BETA1-4 : angle 2.84027 / 1.72 ( 27) link_BETA2-3 : bond 0.00738 / 0.33 ( 3) link_BETA2-3 : angle 6.21268 / 3.30 ( 9) link_NAG-ASN : bond 0.00881 / 0.44 ( 12) link_NAG-ASN : angle 4.85192 / 2.90 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 218 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8029 (pt0) REVERT: H 58 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7513 (tpp-160) REVERT: H 66 GLN cc_start: 0.8108 (mt0) cc_final: 0.7765 (mt0) REVERT: H 68 THR cc_start: 0.8605 (m) cc_final: 0.8395 (m) REVERT: H 81 GLN cc_start: 0.7975 (tt0) cc_final: 0.7505 (tt0) REVERT: L 50 ASP cc_start: 0.8066 (t0) cc_final: 0.7448 (t70) REVERT: A 50 LYS cc_start: 0.8255 (mttm) cc_final: 0.7874 (mttt) REVERT: A 175 LYS cc_start: 0.8691 (mttt) cc_final: 0.8005 (tptp) REVERT: A 196 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.7955 (p0) REVERT: A 294 GLU cc_start: 0.7557 (mp0) cc_final: 0.7329 (mp0) REVERT: A 301 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7911 (ttpt) REVERT: A 331 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7762 (tttt) REVERT: A 459 GLU cc_start: 0.8033 (tt0) cc_final: 0.7658 (tp30) REVERT: A 460 ARG cc_start: 0.8051 (mmm-85) cc_final: 0.7692 (mtp180) REVERT: A 470 LYS cc_start: 0.7968 (tttp) cc_final: 0.7596 (tptt) REVERT: A 475 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7515 (ttmt) REVERT: A 485 LYS cc_start: 0.7644 (tttt) cc_final: 0.7091 (ttpp) REVERT: B 27 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7847 (m-30) REVERT: B 31 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7945 (mp0) REVERT: B 32 LYS cc_start: 0.8580 (mttt) cc_final: 0.7663 (mmtt) REVERT: B 175 LYS cc_start: 0.8701 (mtpp) cc_final: 0.7871 (tptp) REVERT: B 183 ARG cc_start: 0.7470 (mmp-170) cc_final: 0.6965 (mmp80) REVERT: B 199 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: B 237 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8293 (mtt-85) REVERT: B 459 GLU cc_start: 0.8121 (tt0) cc_final: 0.7558 (tp30) REVERT: B 460 ARG cc_start: 0.7774 (mtp180) cc_final: 0.7461 (mtt180) REVERT: B 470 LYS cc_start: 0.7848 (tptm) cc_final: 0.7410 (tptp) REVERT: C 175 LYS cc_start: 0.8805 (mttt) cc_final: 0.7961 (tptp) REVERT: C 196 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.7898 (p0) REVERT: C 237 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8405 (mtt-85) REVERT: C 294 GLU cc_start: 0.8122 (pm20) cc_final: 0.7766 (pm20) REVERT: C 432 GLU cc_start: 0.8651 (tt0) cc_final: 0.8370 (tt0) REVERT: C 438 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8381 (ttt) REVERT: C 460 ARG cc_start: 0.7934 (mtp180) cc_final: 0.7387 (mmt180) REVERT: C 466 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8332 (OUTLIER) REVERT: C 475 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7225 (mtmt) REVERT: C 504 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.5852 (mp0) REVERT: I 58 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8133 (ttm-80) REVERT: I 66 GLN cc_start: 0.8100 (mt0) cc_final: 0.7770 (mt0) REVERT: K 24 ARG cc_start: 0.8053 (mtp180) cc_final: 0.7834 (mtt90) REVERT: K 50 ASP cc_start: 0.8185 (t0) cc_final: 0.7655 (t70) REVERT: D 23 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: D 66 GLN cc_start: 0.8171 (mt0) cc_final: 0.7872 (mt0) REVERT: G 4 LEU cc_start: 0.7988 (mt) cc_final: 0.7732 (tt) REVERT: G 24 ARG cc_start: 0.8116 (mtp180) cc_final: 0.7317 (mtp180) outliers start: 88 outliers final: 47 residues processed: 276 average time/residue: 0.5129 time to fit residues: 158.1007 Evaluate side-chains 271 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 438 MET Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 475 LYS Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 46 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 199 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN D 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.152963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120166 restraints weight = 17964.784| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.00 r_work: 0.3145 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17756 Z= 0.171 Angle : 0.678 13.868 24136 Z= 0.332 Chirality : 0.049 0.477 2657 Planarity : 0.005 0.047 3069 Dihedral : 8.221 81.737 3027 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.64 % Favored : 93.93 % Rotamer: Outliers : 5.05 % Allowed : 19.71 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.18), residues: 2109 helix: 2.07 (0.27), residues: 333 sheet: -0.01 (0.24), residues: 489 loop : -1.44 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 117 TYR 0.011 0.001 TYR C 178 PHE 0.015 0.002 PHE C 156 TRP 0.008 0.001 TRP D 82 HIS 0.010 0.001 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (17705) covalent geometry : angle 0.63056 / 0.32 (24004) SS BOND : bond 0.00446 / 0.29 ( 21) SS BOND : angle 1.98320 / 1.19 ( 42) hydrogen bonds : bond 0.04055 / 2.65 ( 629) hydrogen bonds : angle 5.18110 / 3.58 ( 1791) link_ALPHA1-3 : bond 0.00893 / 0.40 ( 3) link_ALPHA1-3 : angle 2.08734 / 1.20 ( 9) link_BETA1-2 : bond 0.00248 / 0.11 ( 3) link_BETA1-2 : angle 1.09015 / 0.63 ( 9) link_BETA1-4 : bond 0.00406 / 0.28 ( 9) link_BETA1-4 : angle 2.80083 / 1.70 ( 27) link_BETA2-3 : bond 0.00714 / 0.33 ( 3) link_BETA2-3 : angle 6.16818 / 3.27 ( 9) link_NAG-ASN : bond 0.00958 / 0.44 ( 12) link_NAG-ASN : angle 4.66989 / 2.81 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 217 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7946 (pt0) REVERT: H 23 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: H 58 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7260 (tpp-160) REVERT: H 66 GLN cc_start: 0.8076 (mt0) cc_final: 0.7726 (mt0) REVERT: H 68 THR cc_start: 0.8576 (m) cc_final: 0.8363 (m) REVERT: H 81 GLN cc_start: 0.7941 (tt0) cc_final: 0.7462 (tt0) REVERT: L 50 ASP cc_start: 0.8044 (t0) cc_final: 0.7424 (t70) REVERT: A 50 LYS cc_start: 0.8284 (mttm) cc_final: 0.7890 (mttt) REVERT: A 175 LYS cc_start: 0.8675 (mttt) cc_final: 0.7994 (tptp) REVERT: A 196 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8083 (p0) REVERT: A 294 GLU cc_start: 0.7506 (mp0) cc_final: 0.7285 (mp0) REVERT: A 301 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7831 (ttpt) REVERT: A 331 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7723 (tttt) REVERT: A 459 GLU cc_start: 0.8046 (tt0) cc_final: 0.7650 (tp30) REVERT: A 460 ARG cc_start: 0.8026 (mmm-85) cc_final: 0.7666 (mtp180) REVERT: A 470 LYS cc_start: 0.7897 (tttp) cc_final: 0.7520 (tptt) REVERT: A 475 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7414 (ttmt) REVERT: A 485 LYS cc_start: 0.7571 (tttt) cc_final: 0.7012 (ttpp) REVERT: B 31 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7955 (mp0) REVERT: B 32 LYS cc_start: 0.8593 (mttt) cc_final: 0.7653 (mmtt) REVERT: B 175 LYS cc_start: 0.8686 (mtpp) cc_final: 0.7852 (tptp) REVERT: B 183 ARG cc_start: 0.7481 (mmp-170) cc_final: 0.6988 (mmp80) REVERT: B 199 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: B 237 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8255 (mtt-85) REVERT: B 459 GLU cc_start: 0.8110 (tt0) cc_final: 0.7533 (tp30) REVERT: B 460 ARG cc_start: 0.7751 (mtp180) cc_final: 0.7448 (mtt180) REVERT: B 470 LYS cc_start: 0.7774 (tptm) cc_final: 0.7317 (tptp) REVERT: B 508 ASN cc_start: 0.5789 (t0) cc_final: 0.5554 (m110) REVERT: C 79 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7187 (tt0) REVERT: C 175 LYS cc_start: 0.8779 (mttt) cc_final: 0.7946 (tptp) REVERT: C 196 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.7871 (p0) REVERT: C 237 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8394 (mtt-85) REVERT: C 294 GLU cc_start: 0.8115 (pm20) cc_final: 0.7747 (pm20) REVERT: C 432 GLU cc_start: 0.8632 (tt0) cc_final: 0.8396 (tt0) REVERT: C 438 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8363 (ttt) REVERT: C 460 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7322 (mmt180) REVERT: C 466 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8274 (OUTLIER) REVERT: C 475 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7207 (mtmt) REVERT: C 504 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.5827 (mp0) REVERT: I 3 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: I 23 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: I 58 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8100 (ttm-80) REVERT: I 66 GLN cc_start: 0.8065 (mt0) cc_final: 0.7715 (mt0) REVERT: K 4 LEU cc_start: 0.8063 (tp) cc_final: 0.7634 (tt) REVERT: K 24 ARG cc_start: 0.8051 (mtp180) cc_final: 0.7841 (mtt90) REVERT: K 50 ASP cc_start: 0.8153 (t0) cc_final: 0.7627 (t70) REVERT: D 23 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: D 66 GLN cc_start: 0.8138 (mt0) cc_final: 0.7854 (mt0) REVERT: G 4 LEU cc_start: 0.7938 (mt) cc_final: 0.7701 (tt) REVERT: G 24 ARG cc_start: 0.8186 (mtp180) cc_final: 0.7305 (mtp180) outliers start: 93 outliers final: 49 residues processed: 279 average time/residue: 0.5247 time to fit residues: 163.3007 Evaluate side-chains 274 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 206 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 438 MET Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 475 LYS Chi-restraints excluded: chain C residue 492 PHE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 70 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 205 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN D 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.150793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118021 restraints weight = 18101.533| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.02 r_work: 0.3115 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17756 Z= 0.243 Angle : 0.756 13.969 24136 Z= 0.371 Chirality : 0.051 0.418 2657 Planarity : 0.005 0.079 3069 Dihedral : 8.235 76.653 3027 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.78 % Favored : 93.74 % Rotamer: Outliers : 5.37 % Allowed : 19.71 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 2109 helix: 1.92 (0.27), residues: 333 sheet: -0.08 (0.24), residues: 489 loop : -1.46 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 117 TYR 0.014 0.002 TYR C 178 PHE 0.018 0.002 PHE B 156 TRP 0.009 0.002 TRP H 36 HIS 0.009 0.001 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.24 (17705) covalent geometry : angle 0.70692 / 0.36 (24004) SS BOND : bond 0.00544 / 0.34 ( 21) SS BOND : angle 2.56346 / 1.48 ( 42) hydrogen bonds : bond 0.04464 / 2.91 ( 629) hydrogen bonds : angle 5.38206 / 3.72 ( 1791) link_ALPHA1-3 : bond 0.00676 / 0.30 ( 3) link_ALPHA1-3 : angle 2.12440 / 1.22 ( 9) link_BETA1-2 : bond 0.00271 / 0.13 ( 3) link_BETA1-2 : angle 1.28090 / 0.74 ( 9) link_BETA1-4 : bond 0.00391 / 0.27 ( 9) link_BETA1-4 : angle 2.86568 / 1.73 ( 27) link_BETA2-3 : bond 0.01013 / 0.48 ( 3) link_BETA2-3 : angle 6.95995 / 3.69 ( 9) link_NAG-ASN : bond 0.00892 / 0.42 ( 12) link_NAG-ASN : angle 4.74933 / 2.85 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 214 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7504 (mt0) REVERT: H 23 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: H 66 GLN cc_start: 0.8076 (mt0) cc_final: 0.7755 (mt0) REVERT: H 68 THR cc_start: 0.8604 (m) cc_final: 0.8385 (m) REVERT: H 81 GLN cc_start: 0.7980 (tt0) cc_final: 0.7486 (tt0) REVERT: L 24 ARG cc_start: 0.7982 (mtp180) cc_final: 0.7582 (mtp180) REVERT: L 50 ASP cc_start: 0.8072 (t0) cc_final: 0.7427 (t70) REVERT: A 31 GLU cc_start: 0.8094 (tt0) cc_final: 0.7435 (mt-10) REVERT: A 175 LYS cc_start: 0.8727 (mttt) cc_final: 0.8005 (tptp) REVERT: A 294 GLU cc_start: 0.7576 (mp0) cc_final: 0.7358 (mp0) REVERT: A 301 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7843 (ttpt) REVERT: A 331 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7667 (tttt) REVERT: A 459 GLU cc_start: 0.8065 (tt0) cc_final: 0.7640 (tp30) REVERT: A 460 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7706 (mtp180) REVERT: A 470 LYS cc_start: 0.7962 (tttp) cc_final: 0.7516 (tptp) REVERT: A 475 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7395 (ttmt) REVERT: A 485 LYS cc_start: 0.7621 (tttt) cc_final: 0.7057 (ttpp) REVERT: B 32 LYS cc_start: 0.8635 (mttt) cc_final: 0.7617 (mmtt) REVERT: B 175 LYS cc_start: 0.8725 (mtpp) cc_final: 0.7845 (tptp) REVERT: B 183 ARG cc_start: 0.7480 (mmp-170) cc_final: 0.6994 (mmp80) REVERT: B 199 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: B 203 ASN cc_start: 0.8611 (m-40) cc_final: 0.8407 (m-40) REVERT: B 459 GLU cc_start: 0.8198 (tt0) cc_final: 0.7640 (tp30) REVERT: B 460 ARG cc_start: 0.7759 (mtp180) cc_final: 0.7471 (mtt180) REVERT: B 508 ASN cc_start: 0.5938 (t0) cc_final: 0.5632 (m110) REVERT: C 79 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7256 (tt0) REVERT: C 175 LYS cc_start: 0.8824 (mttt) cc_final: 0.7954 (tptp) REVERT: C 237 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8353 (mtt-85) REVERT: C 294 GLU cc_start: 0.8182 (pm20) cc_final: 0.7760 (pm20) REVERT: C 432 GLU cc_start: 0.8645 (tt0) cc_final: 0.8421 (tt0) REVERT: C 438 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8405 (ttt) REVERT: C 475 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7200 (mtmt) REVERT: C 504 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.5871 (mp0) REVERT: C 515 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6567 (tt0) REVERT: I 3 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7416 (mt0) REVERT: I 23 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: I 43 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7701 (mmtm) REVERT: I 58 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8052 (ttm-80) REVERT: I 66 GLN cc_start: 0.8167 (mt0) cc_final: 0.7863 (mt0) REVERT: K 4 LEU cc_start: 0.8084 (tp) cc_final: 0.7659 (tt) REVERT: K 24 ARG cc_start: 0.8046 (mtp180) cc_final: 0.7717 (mtp180) REVERT: K 50 ASP cc_start: 0.8160 (t0) cc_final: 0.7582 (t70) REVERT: D 23 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: D 66 GLN cc_start: 0.8147 (mt0) cc_final: 0.7889 (mt0) REVERT: G 4 LEU cc_start: 0.8013 (mt) cc_final: 0.7776 (tt) REVERT: G 24 ARG cc_start: 0.8216 (mtp180) cc_final: 0.7291 (mtp180) outliers start: 99 outliers final: 49 residues processed: 284 average time/residue: 0.5434 time to fit residues: 172.0366 Evaluate side-chains 274 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 438 MET Chi-restraints excluded: chain C residue 475 LYS Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 515 GLN Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 70 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 100 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 152 optimal weight: 9.9990 chunk 177 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN C 20 ASN I 39 GLN D 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.153870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120581 restraints weight = 18126.123| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.98 r_work: 0.3158 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 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 : 0.003 0.036 17756 Z= 0.130 Angle : 0.647 13.365 24136 Z= 0.318 Chirality : 0.047 0.410 2657 Planarity : 0.004 0.057 3069 Dihedral : 7.872 82.670 3027 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.88 % Favored : 94.69 % Rotamer: Outliers : 3.64 % Allowed : 21.82 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.18), residues: 2109 helix: 2.22 (0.27), residues: 333 sheet: 0.01 (0.25), residues: 477 loop : -1.44 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 117 TYR 0.010 0.001 TYR C 178 PHE 0.017 0.002 PHE C 492 TRP 0.010 0.001 TRP D 82 HIS 0.009 0.001 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (17705) covalent geometry : angle 0.60022 / 0.31 (24004) SS BOND : bond 0.00709 / 0.38 ( 21) SS BOND : angle 2.12746 / 1.26 ( 42) hydrogen bonds : bond 0.03797 / 2.48 ( 629) hydrogen bonds : angle 5.08092 / 3.50 ( 1791) link_ALPHA1-3 : bond 0.00876 / 0.40 ( 3) link_ALPHA1-3 : angle 1.64150 / 0.94 ( 9) link_BETA1-2 : bond 0.00293 / 0.13 ( 3) link_BETA1-2 : angle 0.94840 / 0.54 ( 9) link_BETA1-4 : bond 0.00384 / 0.28 ( 9) link_BETA1-4 : angle 2.72825 / 1.64 ( 27) link_BETA2-3 : bond 0.00614 / 0.29 ( 3) link_BETA2-3 : angle 5.78865 / 3.07 ( 9) link_NAG-ASN : bond 0.00832 / 0.40 ( 12) link_NAG-ASN : angle 4.53069 / 2.73 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 231 time to evaluate : 0.667 Fit side-chains REVERT: H 3 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7924 (pt0) REVERT: H 66 GLN cc_start: 0.8053 (mt0) cc_final: 0.7717 (mt0) REVERT: H 68 THR cc_start: 0.8587 (m) cc_final: 0.8385 (m) REVERT: H 81 GLN cc_start: 0.7959 (tt0) cc_final: 0.7475 (tt0) REVERT: L 50 ASP cc_start: 0.8040 (t0) cc_final: 0.7450 (t70) REVERT: A 31 GLU cc_start: 0.7994 (tt0) cc_final: 0.7347 (mt-10) REVERT: A 50 LYS cc_start: 0.8194 (mttm) cc_final: 0.7813 (mttt) REVERT: A 175 LYS cc_start: 0.8660 (mttt) cc_final: 0.7990 (tptp) REVERT: A 196 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8202 (p0) REVERT: A 301 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7800 (ttpt) REVERT: A 331 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7667 (tttt) REVERT: A 459 GLU cc_start: 0.8015 (tt0) cc_final: 0.7614 (tp30) REVERT: A 460 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7654 (mtp180) REVERT: A 470 LYS cc_start: 0.7853 (tttp) cc_final: 0.7417 (tptp) REVERT: A 475 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7410 (ttmt) REVERT: A 485 LYS cc_start: 0.7566 (tttt) cc_final: 0.7005 (ttpp) REVERT: B 32 LYS cc_start: 0.8636 (mttt) cc_final: 0.7612 (mmtt) REVERT: B 175 LYS cc_start: 0.8654 (mtpp) cc_final: 0.7879 (tptp) REVERT: B 183 ARG cc_start: 0.7445 (mmp-170) cc_final: 0.6924 (mmp80) REVERT: B 196 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8052 (p0) REVERT: B 199 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: B 459 GLU cc_start: 0.8090 (tt0) cc_final: 0.7541 (tp30) REVERT: B 460 ARG cc_start: 0.7763 (mtp180) cc_final: 0.7533 (mmm160) REVERT: B 470 LYS cc_start: 0.7728 (tptm) cc_final: 0.7325 (tptp) REVERT: B 508 ASN cc_start: 0.5832 (t0) cc_final: 0.5552 (m110) REVERT: C 79 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: C 175 LYS cc_start: 0.8752 (mttt) cc_final: 0.7910 (tptp) REVERT: C 196 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.5471 (t0) REVERT: C 294 GLU cc_start: 0.8087 (pm20) cc_final: 0.7687 (pm20) REVERT: C 432 GLU cc_start: 0.8613 (tt0) cc_final: 0.8355 (tt0) REVERT: C 438 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8362 (ttt) REVERT: C 460 ARG cc_start: 0.7843 (mtp180) cc_final: 0.7621 (mmm160) REVERT: C 470 LYS cc_start: 0.7837 (tptm) cc_final: 0.7574 (tptm) REVERT: C 475 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7155 (mtmt) REVERT: C 504 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.5791 (mp0) REVERT: C 515 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6602 (tt0) REVERT: I 58 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8113 (ttm-80) REVERT: I 66 GLN cc_start: 0.8046 (mt0) cc_final: 0.7734 (mt0) REVERT: K 4 LEU cc_start: 0.8033 (tp) cc_final: 0.7594 (tt) REVERT: K 24 ARG cc_start: 0.8042 (mtp180) cc_final: 0.7838 (mtt180) REVERT: K 50 ASP cc_start: 0.8083 (t0) cc_final: 0.7484 (t70) REVERT: D 10 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7184 (mp0) REVERT: D 23 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: D 66 GLN cc_start: 0.8130 (mt0) cc_final: 0.7877 (mt0) REVERT: G 4 LEU cc_start: 0.7914 (mt) cc_final: 0.7678 (tt) REVERT: G 24 ARG cc_start: 0.8161 (mtp180) cc_final: 0.7291 (mtp180) outliers start: 67 outliers final: 30 residues processed: 275 average time/residue: 0.6354 time to fit residues: 194.5806 Evaluate side-chains 265 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 438 MET Chi-restraints excluded: chain C residue 475 LYS Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 515 GLN Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain D residue 23 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 59 optimal weight: 0.1980 chunk 185 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.0010 chunk 184 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN D 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.154027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.121319 restraints weight = 18183.280| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.07 r_work: 0.3155 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17756 Z= 0.131 Angle : 0.658 13.298 24136 Z= 0.325 Chirality : 0.048 0.403 2657 Planarity : 0.004 0.045 3069 Dihedral : 7.771 84.844 3027 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.22 % Favored : 94.31 % Rotamer: Outliers : 3.47 % Allowed : 21.77 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 2109 helix: 2.30 (0.26), residues: 333 sheet: 0.05 (0.25), residues: 483 loop : -1.33 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 117 TYR 0.012 0.001 TYR B 178 PHE 0.017 0.002 PHE C 492 TRP 0.009 0.001 TRP D 82 HIS 0.009 0.001 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (17705) covalent geometry : angle 0.60832 / 0.31 (24004) SS BOND : bond 0.00725 / 0.43 ( 21) SS BOND : angle 2.76836 / 1.74 ( 42) hydrogen bonds : bond 0.03721 / 2.43 ( 629) hydrogen bonds : angle 5.00873 / 3.45 ( 1791) link_ALPHA1-3 : bond 0.00808 / 0.37 ( 3) link_ALPHA1-3 : angle 1.62625 / 0.92 ( 9) link_BETA1-2 : bond 0.00269 / 0.12 ( 3) link_BETA1-2 : angle 0.96272 / 0.55 ( 9) link_BETA1-4 : bond 0.00343 / 0.26 ( 9) link_BETA1-4 : angle 2.69986 / 1.63 ( 27) link_BETA2-3 : bond 0.00566 / 0.27 ( 3) link_BETA2-3 : angle 5.66327 / 3.00 ( 9) link_NAG-ASN : bond 0.00823 / 0.40 ( 12) link_NAG-ASN : angle 4.46087 / 2.70 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 225 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: H 10 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7255 (mp0) REVERT: H 66 GLN cc_start: 0.8063 (mt0) cc_final: 0.7723 (mt0) REVERT: H 81 GLN cc_start: 0.7937 (tt0) cc_final: 0.7442 (tt0) REVERT: L 50 ASP cc_start: 0.8001 (t0) cc_final: 0.7424 (t70) REVERT: A 31 GLU cc_start: 0.8004 (tt0) cc_final: 0.7374 (mt-10) REVERT: A 50 LYS cc_start: 0.8165 (mttm) cc_final: 0.7819 (mtpt) REVERT: A 175 LYS cc_start: 0.8633 (mttt) cc_final: 0.7985 (tptp) REVERT: A 196 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.7948 (p0) REVERT: A 301 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7795 (ttpt) REVERT: A 331 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7680 (tttt) REVERT: A 459 GLU cc_start: 0.8010 (tt0) cc_final: 0.7613 (tp30) REVERT: A 460 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7665 (mtp180) REVERT: A 470 LYS cc_start: 0.7840 (tttp) cc_final: 0.7465 (tptt) REVERT: A 475 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7468 (ttmt) REVERT: A 485 LYS cc_start: 0.7464 (tttt) cc_final: 0.6928 (ttpp) REVERT: B 32 LYS cc_start: 0.8605 (mttt) cc_final: 0.7585 (mmtt) REVERT: B 175 LYS cc_start: 0.8616 (mtpp) cc_final: 0.7866 (tptp) REVERT: B 183 ARG cc_start: 0.7493 (mmp-170) cc_final: 0.6967 (mmp80) REVERT: B 196 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.7756 (p0) REVERT: B 199 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: B 459 GLU cc_start: 0.8061 (tt0) cc_final: 0.7516 (tp30) REVERT: B 460 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7528 (mmm160) REVERT: B 470 LYS cc_start: 0.7736 (tptm) cc_final: 0.7336 (tptp) REVERT: B 508 ASN cc_start: 0.5877 (t0) cc_final: 0.5618 (m110) REVERT: C 79 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7261 (tt0) REVERT: C 175 LYS cc_start: 0.8736 (mttt) cc_final: 0.7908 (tptp) REVERT: C 196 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.5381 (t0) REVERT: C 294 GLU cc_start: 0.8098 (pm20) cc_final: 0.7701 (pm20) REVERT: C 432 GLU cc_start: 0.8641 (tt0) cc_final: 0.8421 (tt0) REVERT: C 438 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8350 (ttt) REVERT: C 460 ARG cc_start: 0.7839 (mtp180) cc_final: 0.7624 (mmm160) REVERT: C 470 LYS cc_start: 0.7848 (tptm) cc_final: 0.7584 (tptm) REVERT: C 475 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7233 (mtmt) REVERT: C 504 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.5767 (mp0) REVERT: C 515 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6603 (tt0) REVERT: I 58 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8158 (ttm-80) REVERT: I 66 GLN cc_start: 0.8110 (mt0) cc_final: 0.7804 (mt0) REVERT: K 4 LEU cc_start: 0.8025 (tp) cc_final: 0.7583 (tt) REVERT: K 24 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7850 (mtt180) REVERT: K 50 ASP cc_start: 0.8110 (t0) cc_final: 0.7558 (t70) REVERT: K 54 ARG cc_start: 0.8436 (ttm110) cc_final: 0.8135 (mtt90) REVERT: D 10 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7232 (mp0) REVERT: D 23 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: D 66 GLN cc_start: 0.8129 (mt0) cc_final: 0.7885 (mt0) REVERT: G 4 LEU cc_start: 0.7893 (mt) cc_final: 0.7653 (tt) REVERT: G 54 ARG cc_start: 0.8406 (ttm110) cc_final: 0.8006 (mtt90) outliers start: 64 outliers final: 37 residues processed: 267 average time/residue: 0.6304 time to fit residues: 188.4510 Evaluate side-chains 269 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 217 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 438 MET Chi-restraints excluded: chain C residue 475 LYS Chi-restraints excluded: chain C residue 492 PHE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 515 GLN Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain D residue 23 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 188 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 120 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 189 optimal weight: 0.9980 chunk 191 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN D 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.155687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122729 restraints weight = 18072.727| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.05 r_work: 0.3177 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17756 Z= 0.115 Angle : 0.633 13.060 24136 Z= 0.313 Chirality : 0.048 0.401 2657 Planarity : 0.004 0.043 3069 Dihedral : 7.682 89.806 3027 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.88 % Favored : 94.64 % Rotamer: Outliers : 2.82 % Allowed : 22.58 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.18), residues: 2109 helix: 2.42 (0.27), residues: 333 sheet: 0.12 (0.25), residues: 483 loop : -1.29 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 117 TYR 0.009 0.001 TYR A 178 PHE 0.015 0.001 PHE C 492 TRP 0.009 0.001 TRP D 82 HIS 0.009 0.001 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (17705) covalent geometry : angle 0.58447 / 0.30 (24004) SS BOND : bond 0.00636 / 0.36 ( 21) SS BOND : angle 2.85607 / 1.68 ( 42) hydrogen bonds : bond 0.03568 / 2.33 ( 629) hydrogen bonds : angle 4.90076 / 3.37 ( 1791) link_ALPHA1-3 : bond 0.00842 / 0.38 ( 3) link_ALPHA1-3 : angle 1.46830 / 0.82 ( 9) link_BETA1-2 : bond 0.00274 / 0.12 ( 3) link_BETA1-2 : angle 0.86390 / 0.50 ( 9) link_BETA1-4 : bond 0.00363 / 0.27 ( 9) link_BETA1-4 : angle 2.61130 / 1.57 ( 27) link_BETA2-3 : bond 0.00566 / 0.27 ( 3) link_BETA2-3 : angle 5.13270 / 2.73 ( 9) link_NAG-ASN : bond 0.00874 / 0.48 ( 12) link_NAG-ASN : angle 4.30568 / 2.61 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: H 10 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7272 (mp0) REVERT: H 56 ASP cc_start: 0.7634 (m-30) cc_final: 0.6500 (t70) REVERT: H 66 GLN cc_start: 0.8105 (mt0) cc_final: 0.7741 (mt0) REVERT: H 81 GLN cc_start: 0.7911 (tt0) cc_final: 0.7427 (tt0) REVERT: L 50 ASP cc_start: 0.7986 (t0) cc_final: 0.7413 (t70) REVERT: A 31 GLU cc_start: 0.7955 (tt0) cc_final: 0.7246 (mt-10) REVERT: A 50 LYS cc_start: 0.8156 (mttm) cc_final: 0.7816 (mtpt) REVERT: A 175 LYS cc_start: 0.8600 (mttt) cc_final: 0.7988 (tptp) REVERT: A 196 ASN cc_start: 0.8398 (p0) cc_final: 0.5230 (t0) REVERT: A 301 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7800 (ttpt) REVERT: A 331 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7684 (tttt) REVERT: A 459 GLU cc_start: 0.7993 (tt0) cc_final: 0.7604 (tp30) REVERT: A 460 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7377 (mmm160) REVERT: A 470 LYS cc_start: 0.7834 (tttp) cc_final: 0.7368 (tptp) REVERT: A 475 LYS cc_start: 0.7913 (mtpp) cc_final: 0.7463 (ttmt) REVERT: A 485 LYS cc_start: 0.7376 (tttt) cc_final: 0.6870 (ttpp) REVERT: B 24 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7624 (mt-10) REVERT: B 32 LYS cc_start: 0.8588 (mttt) cc_final: 0.7613 (mmtt) REVERT: B 175 LYS cc_start: 0.8589 (mtpp) cc_final: 0.7862 (tptp) REVERT: B 183 ARG cc_start: 0.7457 (mmp-170) cc_final: 0.6949 (mmp80) REVERT: B 196 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.5397 (t0) REVERT: B 283 LYS cc_start: 0.1698 (OUTLIER) cc_final: 0.0999 (ptpp) REVERT: B 459 GLU cc_start: 0.7993 (tt0) cc_final: 0.7411 (tp30) REVERT: B 470 LYS cc_start: 0.7699 (tptm) cc_final: 0.7306 (tptp) REVERT: B 475 LYS cc_start: 0.7556 (ttpp) cc_final: 0.7106 (ttmt) REVERT: B 508 ASN cc_start: 0.5862 (t0) cc_final: 0.5641 (m110) REVERT: C 79 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: C 175 LYS cc_start: 0.8727 (mttt) cc_final: 0.7946 (tptp) REVERT: C 196 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.5428 (t0) REVERT: C 334 LYS cc_start: 0.7004 (tmtt) cc_final: 0.6490 (ttpt) REVERT: C 432 GLU cc_start: 0.8634 (tt0) cc_final: 0.8415 (tt0) REVERT: C 438 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8318 (ttt) REVERT: C 460 ARG cc_start: 0.7773 (mtp180) cc_final: 0.7462 (mmm160) REVERT: C 470 LYS cc_start: 0.7851 (tptm) cc_final: 0.7586 (tptm) REVERT: C 475 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7186 (mtmt) REVERT: C 504 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.5722 (mp0) REVERT: C 515 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6599 (tt0) REVERT: I 58 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8158 (ttm-80) REVERT: I 66 GLN cc_start: 0.8123 (mt0) cc_final: 0.7794 (mt0) REVERT: K 4 LEU cc_start: 0.7972 (tp) cc_final: 0.7513 (tt) REVERT: K 24 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7600 (mtp180) REVERT: K 50 ASP cc_start: 0.8066 (t0) cc_final: 0.7525 (t70) REVERT: K 54 ARG cc_start: 0.8385 (ttm110) cc_final: 0.8096 (mtt90) REVERT: D 10 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7275 (mp0) REVERT: D 23 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: D 66 GLN cc_start: 0.8118 (mt0) cc_final: 0.7884 (mt0) REVERT: G 4 LEU cc_start: 0.7834 (mt) cc_final: 0.7602 (tt) REVERT: G 54 ARG cc_start: 0.8400 (ttm110) cc_final: 0.8038 (mtt90) outliers start: 52 outliers final: 30 residues processed: 256 average time/residue: 0.6192 time to fit residues: 176.9591 Evaluate side-chains 262 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 502 CYS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 438 MET Chi-restraints excluded: chain C residue 475 LYS Chi-restraints excluded: chain C residue 492 PHE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 515 GLN Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain D residue 23 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 1 optimal weight: 0.0050 chunk 133 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 195 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN A 20 ASN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.151404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118288 restraints weight = 18068.907| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.06 r_work: 0.3117 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17756 Z= 0.226 Angle : 0.748 14.359 24136 Z= 0.370 Chirality : 0.052 0.391 2657 Planarity : 0.005 0.064 3069 Dihedral : 7.799 79.533 3027 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.74 % Favored : 93.79 % Rotamer: Outliers : 2.93 % Allowed : 22.48 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.18), residues: 2109 helix: 2.12 (0.26), residues: 333 sheet: 0.04 (0.24), residues: 483 loop : -1.29 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 117 TYR 0.015 0.002 TYR G 86 PHE 0.018 0.002 PHE C 156 TRP 0.010 0.002 TRP H 36 HIS 0.009 0.001 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (17705) covalent geometry : angle 0.69897 / 0.36 (24004) SS BOND : bond 0.00803 / 0.45 ( 21) SS BOND : angle 3.18001 / 1.94 ( 42) hydrogen bonds : bond 0.04290 / 2.81 ( 629) hydrogen bonds : angle 5.26648 / 3.64 ( 1791) link_ALPHA1-3 : bond 0.00461 / 0.20 ( 3) link_ALPHA1-3 : angle 1.77167 / 1.01 ( 9) link_BETA1-2 : bond 0.00247 / 0.12 ( 3) link_BETA1-2 : angle 1.12347 / 0.65 ( 9) link_BETA1-4 : bond 0.00377 / 0.28 ( 9) link_BETA1-4 : angle 2.73349 / 1.65 ( 27) link_BETA2-3 : bond 0.00928 / 0.43 ( 3) link_BETA2-3 : angle 6.58909 / 3.49 ( 9) link_NAG-ASN : bond 0.00814 / 0.39 ( 12) link_NAG-ASN : angle 4.41802 / 2.68 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6818.99 seconds wall clock time: 116 minutes 43.59 seconds (7003.59 seconds total)