Starting phenix.real_space_refine on Thu Aug 6 23:36:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zv0_74842/08_2026/9zv0_74842.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zv0_74842/08_2026/9zv0_74842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zv0_74842/08_2026/9zv0_74842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zv0_74842/08_2026/9zv0_74842.map" model { file = "/net/cci-nas-00/data/ceres_data/9zv0_74842/08_2026/9zv0_74842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zv0_74842/08_2026/9zv0_74842.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 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 93 5.16 5 C 11078 2.51 5 N 2937 2.21 5 O 3453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 17561 Number of models: 1 Model: "" Number of chains: 18 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: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain breaks: 1 Chain: "L" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Chain: "D" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "I" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Chain: "G" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain breaks: 1 Chain: "K" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} 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: "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: "H" 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: "D" 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: 3.00, per 1000 atoms: 0.17 Number of scatterers: 17561 At special positions: 0 Unit cell: (117.15, 124.575, 168.3, 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 93 16.00 O 3453 8.00 N 2937 7.00 C 11078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS A 498 " - pdb=" SG CYS A 502 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 326 " distance=2.02 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 302 " - pdb=" SG CYS C 326 " distance=2.01 Simple disulfide: pdb=" SG CYS C 498 " - pdb=" SG CYS C 502 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 104 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 104 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 104 " 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 D 201 " - " ASN D 64 " " NAG G 201 " - " ASN G 64 " " NAG H 201 " - " ASN H 64 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 492.2 milliseconds 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4000 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 58 sheets defined 16.0% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 107 through 115 removed outlier: 3.508A pdb=" N MET A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 205 removed outlier: 3.632A pdb=" N THR A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 413 removed outlier: 3.796A pdb=" N MET A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'A' and resid 441 through 453 removed outlier: 3.850A pdb=" N THR A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 450 " --> pdb=" O TRP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 468 through 478 Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.709A pdb=" N SER A 517 " --> pdb=" O PRO A 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 128 through 133 removed outlier: 4.034A pdb=" N TRP B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.649A pdb=" N THR B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 413 removed outlier: 3.859A pdb=" N MET B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 440 Processing helix chain 'B' and resid 441 through 456 removed outlier: 3.698A pdb=" N THR B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 450 " --> pdb=" O TRP B 446 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 480 removed outlier: 3.704A pdb=" N ARG B 460 " --> pdb=" O MET B 456 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 462 " --> pdb=" O ASN B 458 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 469 " --> pdb=" O HIS B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 509 Processing helix chain 'C' and resid 66 through 72 removed outlier: 3.604A pdb=" N LEU C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 128 through 133 removed outlier: 3.965A pdb=" N TRP C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 205 removed outlier: 3.742A pdb=" N THR C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 413 removed outlier: 3.515A pdb=" N LYS C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 439 removed outlier: 3.503A pdb=" N LEU C 434 " --> pdb=" O ARG C 430 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS C 437 " --> pdb=" O ASN C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 456 removed outlier: 3.818A pdb=" N THR C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 450 " --> pdb=" O TRP C 446 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 481 removed outlier: 3.903A pdb=" N ASP C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 509 Processing helix chain 'C' and resid 513 through 517 Processing helix chain 'L' and resid 95 through 99 removed outlier: 3.530A pdb=" N ASP L 98 " --> pdb=" O ALA L 95 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE L 99 " --> pdb=" O ALA L 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 95 through 99' Processing helix chain 'I' and resid 95 through 99 removed outlier: 3.529A pdb=" N ASP I 98 " --> pdb=" O ALA I 95 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 95 through 99' Processing helix chain 'K' and resid 95 through 99 removed outlier: 3.529A pdb=" N ASP K 98 " --> pdb=" O ALA K 95 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE K 99 " --> pdb=" O ALA K 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 95 through 99' Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.881A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 89 " --> pdb=" O MET A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.454A pdb=" N SER A 104 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N TRP A 244 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU A 189 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR A 266 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 271 " --> pdb=" O HIS A 120 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS A 120 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS A 283 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 118 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.454A pdb=" N SER A 104 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N TRP A 244 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU A 189 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA9, first strand: chain 'A' and resid 143 through 148 removed outlier: 4.543A pdb=" N CYS A 146 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AB2, first strand: chain 'A' and resid 212 through 215 Processing sheet with id=AB3, first strand: chain 'A' and resid 307 through 308 removed outlier: 3.584A pdb=" N ILE A 323 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 13 through 17 removed outlier: 3.762A pdb=" N CYS B 14 " --> pdb=" O HIS B 379 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB6, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'B' and resid 60 through 61 removed outlier: 6.597A pdb=" N LEU B 60 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 89 " --> pdb=" O MET B 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.468A pdb=" N SER B 104 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N TRP B 244 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU B 189 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR B 266 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 271 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N HIS B 120 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS B 283 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE B 118 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.468A pdb=" N SER B 104 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N TRP B 244 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU B 189 " --> pdb=" O PRO B 264 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 137 Processing sheet with id=AC3, first strand: chain 'B' and resid 143 through 148 removed outlier: 4.800A pdb=" N CYS B 146 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 221 through 223 removed outlier: 6.809A pdb=" N LYS B 175 " --> pdb=" O TYR G 118 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR G 118 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AC6, first strand: chain 'B' and resid 484 through 486 Processing sheet with id=AC7, first strand: chain 'C' and resid 16 through 17 removed outlier: 3.593A pdb=" N GLY C 377 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC9, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.995A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.626A pdb=" N SER C 104 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N TRP C 244 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU C 189 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR C 266 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 271 " --> pdb=" O HIS C 120 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N HIS C 120 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS C 283 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE C 118 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.626A pdb=" N SER C 104 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N TRP C 244 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU C 189 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AD6, first strand: chain 'C' and resid 143 through 148 removed outlier: 4.498A pdb=" N CYS C 146 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 252 through 257 removed outlier: 6.803A pdb=" N LYS C 175 " --> pdb=" O TYR D 118 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR D 118 " --> pdb=" O LYS C 175 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 212 through 215 Processing sheet with id=AD9, first strand: chain 'C' and resid 307 through 308 Processing sheet with id=AE1, first strand: chain 'C' and resid 484 through 486 Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AE4, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.112A pdb=" N LEU H 50 " --> pdb=" O SER H 45 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER H 45 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY H 54 " --> pdb=" O TRP H 41 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL H 123 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.112A pdb=" N LEU H 50 " --> pdb=" O SER H 45 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER H 45 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY H 54 " --> pdb=" O TRP H 41 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.625A pdb=" N ASP L 86 " --> pdb=" O SER L 83 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AE8, first strand: chain 'L' and resid 66 through 67 removed outlier: 6.519A pdb=" N TRP L 41 " --> pdb=" O ILE L 53 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AF2, first strand: chain 'D' and resid 66 through 67 removed outlier: 6.554A pdb=" N TRP D 41 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N HIS D 55 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TRP D 39 " --> pdb=" O HIS D 55 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL D 123 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 66 through 67 removed outlier: 6.554A pdb=" N TRP D 41 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N HIS D 55 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TRP D 39 " --> pdb=" O HIS D 55 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 5 through 7 removed outlier: 3.625A pdb=" N ASP I 86 " --> pdb=" O SER I 83 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AF6, first strand: chain 'I' and resid 66 through 67 removed outlier: 6.519A pdb=" N TRP I 41 " --> pdb=" O ILE I 53 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR I 55 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU I 39 " --> pdb=" O TYR I 55 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AF9, first strand: chain 'G' and resid 66 through 67 removed outlier: 6.555A pdb=" N TRP G 41 " --> pdb=" O ILE G 53 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N HIS G 55 " --> pdb=" O TRP G 39 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TRP G 39 " --> pdb=" O HIS G 55 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL G 123 " --> pdb=" O ARG G 106 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 66 through 67 removed outlier: 6.555A pdb=" N TRP G 41 " --> pdb=" O ILE G 53 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N HIS G 55 " --> pdb=" O TRP G 39 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TRP G 39 " --> pdb=" O HIS G 55 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.625A pdb=" N ASP K 86 " --> pdb=" O SER K 83 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AG4, first strand: chain 'K' and resid 66 through 67 removed outlier: 6.519A pdb=" N TRP K 41 " --> pdb=" O ILE K 53 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR K 55 " --> pdb=" O LEU K 39 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU K 39 " --> pdb=" O TYR K 55 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.51: 11715 1.51 - 1.82: 6252 1.82 - 2.13: 5 2.13 - 2.44: 0 2.44 - 2.75: 1 Bond restraints: 17973 Sorted by residual: bond pdb=" C SER D 59 " pdb=" N GLY D 63 " ideal model delta sigma weight residual 1.331 2.749 -1.418 1.54e-02 4.22e+03 8.48e+03 bond pdb=" CA SER A 312 " pdb=" CB SER A 312 " ideal model delta sigma weight residual 1.530 1.475 0.054 1.39e-02 5.18e+03 1.53e+01 bond pdb=" CA SER B 22 " pdb=" CB SER B 22 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.53e-02 4.27e+03 1.30e+01 bond pdb=" CA SER C 312 " pdb=" CB SER C 312 " ideal model delta sigma weight residual 1.537 1.476 0.061 1.85e-02 2.92e+03 1.10e+01 bond pdb=" C ILE B 262 " pdb=" N ALA B 263 " ideal model delta sigma weight residual 1.330 1.281 0.049 1.47e-02 4.63e+03 1.09e+01 ... (remaining 17968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 24247 4.07 - 8.13: 138 8.13 - 12.20: 9 12.20 - 16.27: 1 16.27 - 20.33: 2 Bond angle restraints: 24397 Sorted by residual: angle pdb=" C SER D 59 " pdb=" N GLY D 63 " pdb=" CA GLY D 63 " ideal model delta sigma weight residual 122.69 102.36 20.33 1.59e+00 3.96e-01 1.64e+02 angle pdb=" O SER D 59 " pdb=" C SER D 59 " pdb=" N GLY D 63 " ideal model delta sigma weight residual 122.43 105.79 16.64 1.46e+00 4.69e-01 1.30e+02 angle pdb=" CA SER D 59 " pdb=" C SER D 59 " pdb=" N GLY D 63 " ideal model delta sigma weight residual 118.41 132.10 -13.69 1.34e+00 5.57e-01 1.04e+02 angle pdb=" N VAL A 454 " pdb=" CA VAL A 454 " pdb=" C VAL A 454 " ideal model delta sigma weight residual 113.42 106.27 7.15 1.17e+00 7.31e-01 3.73e+01 angle pdb=" N CYS C 491 " pdb=" CA CYS C 491 " pdb=" C CYS C 491 " ideal model delta sigma weight residual 108.74 117.17 -8.43 1.38e+00 5.25e-01 3.73e+01 ... (remaining 24392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 10243 24.08 - 48.15: 791 48.15 - 72.23: 112 72.23 - 96.30: 19 96.30 - 120.38: 3 Dihedral angle restraints: 11168 sinusoidal: 4908 harmonic: 6260 Sorted by residual: dihedral pdb=" CA PRO I 114 " pdb=" C PRO I 114 " pdb=" N PRO I 115 " pdb=" CA PRO I 115 " ideal model delta harmonic sigma weight residual 180.00 131.58 48.42 0 5.00e+00 4.00e-02 9.38e+01 dihedral pdb=" CA PRO K 114 " pdb=" C PRO K 114 " pdb=" N PRO K 115 " pdb=" CA PRO K 115 " ideal model delta harmonic sigma weight residual 180.00 131.60 48.40 0 5.00e+00 4.00e-02 9.37e+01 dihedral pdb=" CA PRO L 114 " pdb=" C PRO L 114 " pdb=" N PRO L 115 " pdb=" CA PRO L 115 " ideal model delta harmonic sigma weight residual 180.00 131.62 48.38 0 5.00e+00 4.00e-02 9.36e+01 ... (remaining 11165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2372 0.083 - 0.166: 323 0.166 - 0.250: 33 0.250 - 0.333: 4 0.333 - 0.416: 6 Chirality restraints: 2738 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 -2.86 0.36 2.00e-02 2.50e+03 3.18e+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 -2.84 0.34 2.00e-02 2.50e+03 2.87e+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 -2.81 0.31 2.00e-02 2.50e+03 2.35e+02 ... (remaining 2735 not shown) Planarity restraints: 3115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 603 " -0.318 2.00e-02 2.50e+03 2.77e-01 9.60e+02 pdb=" C7 NAG C 603 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG C 603 " -0.125 2.00e-02 2.50e+03 pdb=" N2 NAG C 603 " 0.497 2.00e-02 2.50e+03 pdb=" O7 NAG C 603 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 201 " 0.294 2.00e-02 2.50e+03 2.51e-01 7.90e+02 pdb=" C7 NAG D 201 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG D 201 " 0.175 2.00e-02 2.50e+03 pdb=" N2 NAG D 201 " -0.438 2.00e-02 2.50e+03 pdb=" O7 NAG D 201 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 201 " 0.262 2.00e-02 2.50e+03 2.24e-01 6.30e+02 pdb=" C7 NAG G 201 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG G 201 " 0.162 2.00e-02 2.50e+03 pdb=" N2 NAG G 201 " -0.390 2.00e-02 2.50e+03 pdb=" O7 NAG G 201 " 0.030 2.00e-02 2.50e+03 ... (remaining 3112 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 6045 2.86 - 3.37: 14370 3.37 - 3.88: 29219 3.88 - 4.39: 34308 4.39 - 4.90: 60609 Nonbonded interactions: 144551 Sorted by model distance: nonbonded pdb=" O5 MAN F 4 " pdb=" O6 MAN F 4 " model vdw 2.350 2.432 nonbonded pdb=" O5 MAN E 4 " pdb=" O6 MAN E 4 " model vdw 2.353 2.432 nonbonded pdb=" C3 MAN J 4 " pdb=" O5 MAN J 4 " model vdw 2.535 2.776 nonbonded pdb=" O THR G 65 " pdb=" OG1 THR G 65 " model vdw 2.540 3.040 nonbonded pdb=" C SER B 467 " pdb=" OG SER B 467 " model vdw 2.553 2.616 ... (remaining 144546 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 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'I' 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: 3.410 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.490 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 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 : 0.013 1.418 18024 Z= 0.768 Angle : 0.995 20.334 24529 Z= 0.582 Chirality : 0.060 0.416 2738 Planarity : 0.012 0.277 3103 Dihedral : 16.049 120.375 7105 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.15 % Favored : 93.43 % Rotamer: Outliers : 2.96 % Allowed : 19.39 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -2.78 (0.17), residues: 2130 helix: -1.71 (0.28), residues: 333 sheet: -1.98 (0.20), residues: 624 loop : -1.76 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 92 TYR 0.025 0.002 TYR C 511 PHE 0.020 0.002 PHE B 363 TRP 0.019 0.002 TRP G 52 HIS 0.011 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.01279 / 0.77 (17973) covalent geometry : angle 0.96625 / 0.58 (24397) SS BOND : bond 0.00722 / 0.41 ( 21) SS BOND : angle 2.75022 / 1.64 ( 42) hydrogen bonds : bond 0.22585 / 15.45 ( 512) hydrogen bonds : angle 9.77056 / 6.89 ( 1521) link_ALPHA1-3 : bond 0.00665 / 0.33 ( 3) link_ALPHA1-3 : angle 1.74897 / 0.79 ( 9) link_BETA1-2 : bond 0.00232 / 0.12 ( 3) link_BETA1-2 : angle 1.96262 / 1.56 ( 9) link_BETA1-4 : bond 0.00488 / 0.27 ( 9) link_BETA1-4 : angle 2.76649 / 1.80 ( 27) link_BETA2-3 : bond 0.00114 / 0.06 ( 3) link_BETA2-3 : angle 7.35138 / 4.42 ( 9) link_NAG-ASN : bond 0.00648 / 0.34 ( 12) link_NAG-ASN : angle 3.46828 / 2.15 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8252 (mtt) REVERT: A 52 CYS cc_start: 0.6225 (m) cc_final: 0.5991 (m) REVERT: A 76 MET cc_start: 0.8214 (mmp) cc_final: 0.7421 (mtm) REVERT: A 106 ASN cc_start: 0.7900 (t0) cc_final: 0.7394 (t0) REVERT: A 186 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7146 (mp) REVERT: A 312 SER cc_start: 0.9188 (m) cc_final: 0.8892 (p) REVERT: A 411 ASP cc_start: 0.7823 (m-30) cc_final: 0.7501 (t0) REVERT: A 415 THR cc_start: 0.8343 (p) cc_final: 0.8143 (t) REVERT: A 436 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7161 (ttmt) REVERT: A 440 ASP cc_start: 0.7859 (m-30) cc_final: 0.7447 (t70) REVERT: A 456 MET cc_start: 0.8479 (mtm) cc_final: 0.8178 (mtp) REVERT: A 460 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7830 (mtp85) REVERT: A 485 LYS cc_start: 0.8674 (mtpt) cc_final: 0.7987 (mttm) REVERT: B 20 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.7107 (p0) REVERT: B 76 MET cc_start: 0.8495 (mmp) cc_final: 0.7630 (mtm) REVERT: B 200 GLU cc_start: 0.7555 (tt0) cc_final: 0.7086 (tt0) REVERT: B 282 LYS cc_start: 0.7992 (tttt) cc_final: 0.7699 (tttp) REVERT: B 301 LYS cc_start: 0.8286 (mttt) cc_final: 0.7997 (mttm) REVERT: B 413 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.6755 (mmt) REVERT: B 437 LYS cc_start: 0.8103 (mmtp) cc_final: 0.7462 (mtpp) REVERT: B 440 ASP cc_start: 0.8630 (t0) cc_final: 0.8052 (t70) REVERT: B 460 ARG cc_start: 0.7848 (mtt90) cc_final: 0.7411 (mtp85) REVERT: B 485 LYS cc_start: 0.8409 (ttpt) cc_final: 0.7875 (ttmm) REVERT: C 57 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8073 (m) REVERT: C 76 MET cc_start: 0.8311 (mmp) cc_final: 0.7432 (mtm) REVERT: C 106 ASN cc_start: 0.7807 (t0) cc_final: 0.7445 (t0) REVERT: C 209 ILE cc_start: 0.8187 (mt) cc_final: 0.7895 (mm) REVERT: C 311 SER cc_start: 0.9053 (t) cc_final: 0.8750 (p) REVERT: C 312 SER cc_start: 0.9026 (m) cc_final: 0.8814 (p) REVERT: C 328 LYS cc_start: 0.8323 (mmtt) cc_final: 0.7944 (mmtm) REVERT: C 376 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: C 423 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7518 (mp0) REVERT: C 436 LYS cc_start: 0.8290 (tmtt) cc_final: 0.7332 (ttmt) REVERT: C 439 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7824 (mt-10) REVERT: C 440 ASP cc_start: 0.8527 (t0) cc_final: 0.7815 (t70) REVERT: C 456 MET cc_start: 0.8562 (mtm) cc_final: 0.8300 (mtm) REVERT: C 485 LYS cc_start: 0.8134 (tttt) cc_final: 0.7427 (ttmm) outliers start: 56 outliers final: 35 residues processed: 277 average time/residue: 0.1260 time to fit residues: 51.5518 Evaluate side-chains 263 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 376 TYR Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 36 TYR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 79 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS A 38 HIS A 254 HIS B 20 ASN B 254 HIS B 426 ASN C 254 HIS I 27 GLN K 27 GLN K 48 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.111289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.083648 restraints weight = 22141.439| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 1.93 r_work: 0.2667 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18024 Z= 0.164 Angle : 0.655 8.231 24529 Z= 0.328 Chirality : 0.047 0.320 2738 Planarity : 0.005 0.074 3103 Dihedral : 10.097 110.345 3124 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.04 % Rotamer: Outliers : 3.59 % Allowed : 18.86 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -2.29 (0.18), residues: 2132 helix: -1.16 (0.29), residues: 333 sheet: -1.49 (0.21), residues: 618 loop : -1.62 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 92 TYR 0.015 0.001 TYR K 55 PHE 0.017 0.001 PHE D 87 TRP 0.018 0.001 TRP G 52 HIS 0.012 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (17973) covalent geometry : angle 0.62315 / 0.32 (24397) SS BOND : bond 0.00460 / 0.28 ( 21) SS BOND : angle 1.93408 / 1.14 ( 42) hydrogen bonds : bond 0.04262 / 2.86 ( 512) hydrogen bonds : angle 6.20739 / 4.47 ( 1521) link_ALPHA1-3 : bond 0.00731 / 0.37 ( 3) link_ALPHA1-3 : angle 2.04982 / 0.99 ( 9) link_BETA1-2 : bond 0.00165 / 0.08 ( 3) link_BETA1-2 : angle 1.71545 / 1.31 ( 9) link_BETA1-4 : bond 0.00361 / 0.20 ( 9) link_BETA1-4 : angle 2.79163 / 1.80 ( 27) link_BETA2-3 : bond 0.00976 / 0.49 ( 3) link_BETA2-3 : angle 5.75020 / 3.12 ( 9) link_NAG-ASN : bond 0.00529 / 0.32 ( 12) link_NAG-ASN : angle 2.98131 / 2.00 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 230 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 52 CYS cc_start: 0.7553 (m) cc_final: 0.7235 (m) REVERT: A 76 MET cc_start: 0.8434 (mmp) cc_final: 0.7709 (mtm) REVERT: A 106 ASN cc_start: 0.8225 (t0) cc_final: 0.7875 (t0) REVERT: A 146 CYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8111 (m) REVERT: A 186 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 200 GLU cc_start: 0.8393 (tt0) cc_final: 0.8179 (tt0) REVERT: A 312 SER cc_start: 0.9105 (m) cc_final: 0.8677 (t) REVERT: A 411 ASP cc_start: 0.8008 (m-30) cc_final: 0.7787 (t0) REVERT: A 436 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7477 (ttmt) REVERT: A 440 ASP cc_start: 0.7849 (m-30) cc_final: 0.7643 (t70) REVERT: A 456 MET cc_start: 0.8608 (mtm) cc_final: 0.8354 (mtp) REVERT: A 460 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.8105 (mtp85) REVERT: A 485 LYS cc_start: 0.8464 (mtpt) cc_final: 0.7903 (ttmm) REVERT: B 32 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8468 (mmtt) REVERT: B 76 MET cc_start: 0.8587 (mmp) cc_final: 0.7820 (mtm) REVERT: B 200 GLU cc_start: 0.8514 (tt0) cc_final: 0.8030 (tt0) REVERT: B 282 LYS cc_start: 0.8748 (tttt) cc_final: 0.8507 (tttp) REVERT: B 301 LYS cc_start: 0.8428 (mttt) cc_final: 0.8117 (mttm) REVERT: B 312 SER cc_start: 0.8786 (m) cc_final: 0.8533 (t) REVERT: B 413 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7297 (mmt) REVERT: B 437 LYS cc_start: 0.8377 (mmtp) cc_final: 0.7745 (mtpp) REVERT: B 440 ASP cc_start: 0.8630 (t0) cc_final: 0.7976 (t70) REVERT: B 460 ARG cc_start: 0.8126 (mtt90) cc_final: 0.7609 (mtp85) REVERT: B 485 LYS cc_start: 0.7938 (ttpt) cc_final: 0.7396 (ttmm) REVERT: C 76 MET cc_start: 0.8520 (mmp) cc_final: 0.7668 (mtm) REVERT: C 106 ASN cc_start: 0.8039 (t0) cc_final: 0.7760 (t0) REVERT: C 209 ILE cc_start: 0.8890 (mt) cc_final: 0.8689 (mm) REVERT: C 311 SER cc_start: 0.8683 (t) cc_final: 0.8443 (p) REVERT: C 312 SER cc_start: 0.9005 (m) cc_final: 0.8714 (t) REVERT: C 376 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: C 423 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7821 (mp0) REVERT: C 436 LYS cc_start: 0.8545 (tmtt) cc_final: 0.7672 (ttmt) REVERT: C 440 ASP cc_start: 0.8705 (t0) cc_final: 0.7978 (t70) REVERT: C 456 MET cc_start: 0.8664 (mtm) cc_final: 0.8338 (mtp) REVERT: C 485 LYS cc_start: 0.7773 (tttt) cc_final: 0.7045 (ttmm) REVERT: C 504 GLU cc_start: 0.7963 (tp30) cc_final: 0.7375 (tp30) REVERT: D 92 ARG cc_start: 0.8313 (mtm180) cc_final: 0.8076 (mtt90) outliers start: 68 outliers final: 41 residues processed: 291 average time/residue: 0.1343 time to fit residues: 59.2129 Evaluate side-chains 267 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 376 TYR Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain I residue 36 TYR Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 39 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 ASN B 48 ASN B 426 ASN I 27 GLN K 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.160331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.134833 restraints weight = 20083.998| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.73 r_work: 0.2782 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18024 Z= 0.159 Angle : 0.616 7.842 24529 Z= 0.307 Chirality : 0.046 0.349 2738 Planarity : 0.005 0.078 3103 Dihedral : 9.583 107.054 3104 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 4.49 % Allowed : 17.80 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.92 (0.18), residues: 2132 helix: -0.83 (0.30), residues: 333 sheet: -1.02 (0.22), residues: 606 loop : -1.53 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 92 TYR 0.014 0.001 TYR A 516 PHE 0.017 0.001 PHE H 87 TRP 0.017 0.001 TRP G 52 HIS 0.007 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (17973) covalent geometry : angle 0.58812 / 0.30 (24397) SS BOND : bond 0.00464 / 0.29 ( 21) SS BOND : angle 1.91919 / 1.14 ( 42) hydrogen bonds : bond 0.03547 / 2.37 ( 512) hydrogen bonds : angle 5.60555 / 4.05 ( 1521) link_ALPHA1-3 : bond 0.00806 / 0.40 ( 3) link_ALPHA1-3 : angle 1.89834 / 0.96 ( 9) link_BETA1-2 : bond 0.00131 / 0.07 ( 3) link_BETA1-2 : angle 1.62812 / 1.21 ( 9) link_BETA1-4 : bond 0.00357 / 0.20 ( 9) link_BETA1-4 : angle 2.73316 / 1.76 ( 27) link_BETA2-3 : bond 0.00823 / 0.41 ( 3) link_BETA2-3 : angle 5.49061 / 3.00 ( 9) link_NAG-ASN : bond 0.00388 / 0.24 ( 12) link_NAG-ASN : angle 2.23783 / 1.47 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 230 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8354 (mmp) cc_final: 0.7660 (mtm) REVERT: A 106 ASN cc_start: 0.8122 (t0) cc_final: 0.7752 (t0) REVERT: A 146 CYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7992 (m) REVERT: A 200 GLU cc_start: 0.8378 (tt0) cc_final: 0.8083 (tt0) REVERT: A 312 SER cc_start: 0.9031 (m) cc_final: 0.8647 (t) REVERT: A 411 ASP cc_start: 0.7938 (m-30) cc_final: 0.7691 (t0) REVERT: A 436 LYS cc_start: 0.8078 (ttpt) cc_final: 0.7423 (ttmt) REVERT: A 440 ASP cc_start: 0.7767 (m-30) cc_final: 0.7548 (t70) REVERT: A 456 MET cc_start: 0.8525 (mtm) cc_final: 0.8274 (mtp) REVERT: A 485 LYS cc_start: 0.8428 (mtpt) cc_final: 0.7906 (ttmm) REVERT: B 32 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8379 (mmtt) REVERT: B 76 MET cc_start: 0.8485 (mmp) cc_final: 0.7748 (mtm) REVERT: B 200 GLU cc_start: 0.8525 (tt0) cc_final: 0.8032 (tt0) REVERT: B 282 LYS cc_start: 0.8670 (tttt) cc_final: 0.8460 (tttp) REVERT: B 301 LYS cc_start: 0.8480 (mttt) cc_final: 0.8214 (mttm) REVERT: B 437 LYS cc_start: 0.8284 (mmtp) cc_final: 0.7720 (mmmt) REVERT: B 440 ASP cc_start: 0.8492 (t0) cc_final: 0.7708 (t70) REVERT: B 460 ARG cc_start: 0.7972 (mtt90) cc_final: 0.7514 (mtp85) REVERT: B 485 LYS cc_start: 0.7887 (ttpt) cc_final: 0.7364 (ttmm) REVERT: C 76 MET cc_start: 0.8398 (mmp) cc_final: 0.7654 (mtm) REVERT: C 106 ASN cc_start: 0.7931 (t0) cc_final: 0.7629 (t0) REVERT: C 209 ILE cc_start: 0.8868 (mt) cc_final: 0.8655 (mm) REVERT: C 311 SER cc_start: 0.8527 (t) cc_final: 0.8248 (p) REVERT: C 312 SER cc_start: 0.8879 (m) cc_final: 0.8655 (t) REVERT: C 376 TYR cc_start: 0.9153 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: C 413 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.7538 (mtp) REVERT: C 423 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7792 (mp0) REVERT: C 436 LYS cc_start: 0.8444 (tmtt) cc_final: 0.7609 (ttmt) REVERT: C 440 ASP cc_start: 0.8583 (t0) cc_final: 0.7798 (t70) REVERT: C 456 MET cc_start: 0.8634 (mtm) cc_final: 0.8299 (mtp) REVERT: C 485 LYS cc_start: 0.7607 (tttt) cc_final: 0.6855 (ttmm) REVERT: C 504 GLU cc_start: 0.7894 (tp30) cc_final: 0.7362 (tp30) REVERT: G 52 TRP cc_start: 0.9050 (OUTLIER) cc_final: 0.8817 (t60) outliers start: 85 outliers final: 59 residues processed: 302 average time/residue: 0.1292 time to fit residues: 59.2240 Evaluate side-chains 271 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 502 CYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 115 LEU 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 200 GLU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 376 TYR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 52 TRP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 36 TYR Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 39 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 52 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 426 ASN C 47 HIS C 426 ASN I 27 GLN K 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.113165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.087364 restraints weight = 22192.241| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.66 r_work: 0.2741 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 18024 Z= 0.228 Angle : 0.662 8.129 24529 Z= 0.331 Chirality : 0.047 0.250 2738 Planarity : 0.005 0.081 3103 Dihedral : 9.477 106.947 3100 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.80 % Favored : 93.01 % Rotamer: Outliers : 5.12 % Allowed : 17.75 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.80 (0.18), residues: 2132 helix: -0.62 (0.30), residues: 330 sheet: -0.99 (0.22), residues: 600 loop : -1.45 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 230 TYR 0.017 0.002 TYR K 55 PHE 0.019 0.002 PHE G 87 TRP 0.020 0.002 TRP G 52 HIS 0.008 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.23 (17973) covalent geometry : angle 0.63186 / 0.32 (24397) SS BOND : bond 0.00501 / 0.31 ( 21) SS BOND : angle 2.68637 / 1.68 ( 42) hydrogen bonds : bond 0.03565 / 2.39 ( 512) hydrogen bonds : angle 5.46859 / 3.95 ( 1521) link_ALPHA1-3 : bond 0.00634 / 0.32 ( 3) link_ALPHA1-3 : angle 1.77003 / 0.94 ( 9) link_BETA1-2 : bond 0.00192 / 0.10 ( 3) link_BETA1-2 : angle 1.67028 / 1.27 ( 9) link_BETA1-4 : bond 0.00347 / 0.20 ( 9) link_BETA1-4 : angle 2.73835 / 1.78 ( 27) link_BETA2-3 : bond 0.00951 / 0.48 ( 3) link_BETA2-3 : angle 5.94468 / 3.35 ( 9) link_NAG-ASN : bond 0.00322 / 0.22 ( 12) link_NAG-ASN : angle 1.93337 / 1.22 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 222 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8105 (t0) cc_final: 0.7855 (t0) REVERT: A 76 MET cc_start: 0.8382 (mmp) cc_final: 0.7686 (mtm) REVERT: A 106 ASN cc_start: 0.8141 (t0) cc_final: 0.7781 (t0) REVERT: A 146 CYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8037 (m) REVERT: A 200 GLU cc_start: 0.8492 (tt0) cc_final: 0.8272 (tt0) REVERT: A 312 SER cc_start: 0.8946 (m) cc_final: 0.8611 (t) REVERT: A 411 ASP cc_start: 0.8041 (m-30) cc_final: 0.7776 (t0) REVERT: A 456 MET cc_start: 0.8557 (mtm) cc_final: 0.8261 (mtp) REVERT: A 485 LYS cc_start: 0.8501 (mtpt) cc_final: 0.7956 (ttmm) REVERT: B 32 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8368 (mmtt) REVERT: B 76 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7803 (mtm) REVERT: B 200 GLU cc_start: 0.8572 (tt0) cc_final: 0.8081 (tt0) REVERT: B 241 ASP cc_start: 0.8793 (m-30) cc_final: 0.8522 (m-30) REVERT: B 301 LYS cc_start: 0.8538 (mttt) cc_final: 0.8265 (mttm) REVERT: B 437 LYS cc_start: 0.8358 (mmtp) cc_final: 0.7802 (mmmt) REVERT: B 440 ASP cc_start: 0.8555 (t0) cc_final: 0.7752 (t70) REVERT: B 460 ARG cc_start: 0.7956 (mtt90) cc_final: 0.7611 (mtp85) REVERT: B 485 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7488 (ptmm) REVERT: C 76 MET cc_start: 0.8412 (mmp) cc_final: 0.7681 (mtm) REVERT: C 106 ASN cc_start: 0.7983 (t0) cc_final: 0.7694 (t0) REVERT: C 311 SER cc_start: 0.8628 (t) cc_final: 0.8333 (p) REVERT: C 328 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8194 (mmtm) REVERT: C 376 TYR cc_start: 0.9222 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: C 423 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7862 (mp0) REVERT: C 436 LYS cc_start: 0.8515 (tmtt) cc_final: 0.7671 (ttmt) REVERT: C 440 ASP cc_start: 0.8671 (t0) cc_final: 0.7889 (t70) REVERT: C 456 MET cc_start: 0.8696 (mtm) cc_final: 0.8412 (mtm) REVERT: C 485 LYS cc_start: 0.7738 (tttt) cc_final: 0.7053 (ttmm) REVERT: C 504 GLU cc_start: 0.7993 (tp30) cc_final: 0.7494 (tp30) REVERT: G 52 TRP cc_start: 0.9121 (OUTLIER) cc_final: 0.8856 (t60) outliers start: 97 outliers final: 76 residues processed: 305 average time/residue: 0.1391 time to fit residues: 64.7796 Evaluate side-chains 286 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 206 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 502 CYS Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 376 TYR Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 52 TRP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 36 TYR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 39 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 124 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 426 ASN C 426 ASN C 479 GLN K 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.108607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.082186 restraints weight = 22292.283| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 1.77 r_work: 0.2645 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 18024 Z= 0.233 Angle : 0.656 8.274 24529 Z= 0.327 Chirality : 0.047 0.224 2738 Planarity : 0.005 0.082 3103 Dihedral : 9.350 105.240 3093 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.75 % Favored : 93.06 % Rotamer: Outliers : 5.76 % Allowed : 17.38 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.75 (0.18), residues: 2132 helix: -0.59 (0.30), residues: 333 sheet: -0.96 (0.22), residues: 606 loop : -1.42 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 481 TYR 0.015 0.002 TYR I 55 PHE 0.018 0.002 PHE G 87 TRP 0.020 0.002 TRP G 52 HIS 0.006 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.23 (17973) covalent geometry : angle 0.62626 / 0.32 (24397) SS BOND : bond 0.00507 / 0.31 ( 21) SS BOND : angle 2.66752 / 1.56 ( 42) hydrogen bonds : bond 0.03470 / 2.32 ( 512) hydrogen bonds : angle 5.37351 / 3.89 ( 1521) link_ALPHA1-3 : bond 0.00610 / 0.31 ( 3) link_ALPHA1-3 : angle 1.70384 / 0.94 ( 9) link_BETA1-2 : bond 0.00174 / 0.09 ( 3) link_BETA1-2 : angle 1.63523 / 1.24 ( 9) link_BETA1-4 : bond 0.00332 / 0.19 ( 9) link_BETA1-4 : angle 2.74884 / 1.78 ( 27) link_BETA2-3 : bond 0.00928 / 0.47 ( 3) link_BETA2-3 : angle 6.02403 / 3.39 ( 9) link_NAG-ASN : bond 0.00317 / 0.22 ( 12) link_NAG-ASN : angle 1.79629 / 1.12 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 222 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7589 (mtm) REVERT: A 106 ASN cc_start: 0.8145 (t0) cc_final: 0.7733 (t0) REVERT: A 146 CYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7895 (m) REVERT: A 200 GLU cc_start: 0.8416 (tt0) cc_final: 0.8200 (tt0) REVERT: A 312 SER cc_start: 0.8949 (m) cc_final: 0.8620 (t) REVERT: A 411 ASP cc_start: 0.7990 (m-30) cc_final: 0.7693 (t0) REVERT: A 456 MET cc_start: 0.8542 (mtm) cc_final: 0.8237 (mtp) REVERT: A 485 LYS cc_start: 0.8451 (mtpt) cc_final: 0.7893 (ttmm) REVERT: A 510 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8459 (p) REVERT: B 32 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8350 (mmtt) REVERT: B 76 MET cc_start: 0.8440 (mmp) cc_final: 0.7786 (mpp) REVERT: B 157 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7880 (mtp180) REVERT: B 200 GLU cc_start: 0.8540 (tt0) cc_final: 0.7992 (tt0) REVERT: B 241 ASP cc_start: 0.8723 (m-30) cc_final: 0.8407 (m-30) REVERT: B 301 LYS cc_start: 0.8522 (mttt) cc_final: 0.8229 (mttm) REVERT: B 437 LYS cc_start: 0.8233 (mmtp) cc_final: 0.7648 (mttt) REVERT: B 440 ASP cc_start: 0.8583 (t0) cc_final: 0.8248 (t70) REVERT: B 460 ARG cc_start: 0.7887 (mtt90) cc_final: 0.7477 (mtp85) REVERT: C 76 MET cc_start: 0.8413 (mmp) cc_final: 0.7542 (mtm) REVERT: C 106 ASN cc_start: 0.8021 (t0) cc_final: 0.7674 (t0) REVERT: C 376 TYR cc_start: 0.9239 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: C 413 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.7468 (mtp) REVERT: C 416 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8668 (mt0) REVERT: C 423 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7771 (mp0) REVERT: C 436 LYS cc_start: 0.8377 (tmtt) cc_final: 0.7503 (ttmt) REVERT: C 440 ASP cc_start: 0.8591 (t0) cc_final: 0.8376 (t70) REVERT: C 456 MET cc_start: 0.8621 (mtm) cc_final: 0.8326 (mtm) REVERT: C 504 GLU cc_start: 0.7947 (tp30) cc_final: 0.7173 (tp30) REVERT: C 508 ASN cc_start: 0.7807 (t0) cc_final: 0.7437 (m-40) REVERT: G 43 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7043 (ttp-170) REVERT: G 52 TRP cc_start: 0.9075 (OUTLIER) cc_final: 0.8684 (t60) outliers start: 109 outliers final: 81 residues processed: 316 average time/residue: 0.1314 time to fit residues: 63.8135 Evaluate side-chains 298 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 208 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 502 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 376 TYR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 416 GLN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 52 TRP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 36 TYR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 39 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 140 optimal weight: 0.0020 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.0070 chunk 160 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 426 ASN C 433 ASN K 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.112892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.086442 restraints weight = 21941.899| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 1.78 r_work: 0.2711 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18024 Z= 0.103 Angle : 0.561 7.606 24529 Z= 0.279 Chirality : 0.045 0.216 2738 Planarity : 0.005 0.081 3103 Dihedral : 8.780 100.659 3086 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 4.49 % Allowed : 18.65 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.44 (0.18), residues: 2132 helix: -0.12 (0.31), residues: 330 sheet: -0.72 (0.22), residues: 606 loop : -1.31 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 481 TYR 0.013 0.001 TYR D 117 PHE 0.013 0.001 PHE B 363 TRP 0.014 0.001 TRP G 52 HIS 0.005 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (17973) covalent geometry : angle 0.53708 / 0.27 (24397) SS BOND : bond 0.00293 / 0.18 ( 21) SS BOND : angle 1.73374 / 1.03 ( 42) hydrogen bonds : bond 0.02939 / 1.95 ( 512) hydrogen bonds : angle 5.02328 / 3.63 ( 1521) link_ALPHA1-3 : bond 0.00905 / 0.45 ( 3) link_ALPHA1-3 : angle 1.61719 / 0.94 ( 9) link_BETA1-2 : bond 0.00107 / 0.05 ( 3) link_BETA1-2 : angle 1.40885 / 0.99 ( 9) link_BETA1-4 : bond 0.00349 / 0.20 ( 9) link_BETA1-4 : angle 2.74959 / 1.76 ( 27) link_BETA2-3 : bond 0.00642 / 0.32 ( 3) link_BETA2-3 : angle 4.86489 / 2.60 ( 9) link_NAG-ASN : bond 0.00311 / 0.21 ( 12) link_NAG-ASN : angle 1.62079 / 1.05 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 230 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8362 (mmp) cc_final: 0.7645 (mtm) REVERT: A 106 ASN cc_start: 0.8120 (t0) cc_final: 0.7722 (t0) REVERT: A 146 CYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7901 (m) REVERT: A 209 ILE cc_start: 0.8982 (mm) cc_final: 0.8777 (mm) REVERT: A 312 SER cc_start: 0.8814 (m) cc_final: 0.8555 (t) REVERT: A 371 MET cc_start: 0.8547 (ttt) cc_final: 0.8283 (ttt) REVERT: A 373 ASP cc_start: 0.7953 (p0) cc_final: 0.7626 (t0) REVERT: A 411 ASP cc_start: 0.7936 (m-30) cc_final: 0.7717 (t0) REVERT: A 456 MET cc_start: 0.8427 (mtm) cc_final: 0.8148 (mtp) REVERT: A 485 LYS cc_start: 0.8465 (mtpt) cc_final: 0.7883 (ttmm) REVERT: A 510 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8442 (p) REVERT: B 32 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8323 (mmtt) REVERT: B 76 MET cc_start: 0.8403 (mmp) cc_final: 0.7761 (mpp) REVERT: B 157 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7730 (mtp180) REVERT: B 183 ARG cc_start: 0.8039 (tpm170) cc_final: 0.7766 (tpp-160) REVERT: B 200 GLU cc_start: 0.8487 (tt0) cc_final: 0.7918 (tt0) REVERT: B 301 LYS cc_start: 0.8465 (mttt) cc_final: 0.8215 (mttm) REVERT: B 371 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8101 (ttp) REVERT: B 437 LYS cc_start: 0.8180 (mmtp) cc_final: 0.7577 (mttt) REVERT: B 440 ASP cc_start: 0.8426 (t0) cc_final: 0.7697 (t70) REVERT: B 460 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7418 (mtp85) REVERT: C 30 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8339 (mmt) REVERT: C 76 MET cc_start: 0.8404 (mmp) cc_final: 0.7544 (mtm) REVERT: C 106 ASN cc_start: 0.8006 (t0) cc_final: 0.7685 (t0) REVERT: C 209 ILE cc_start: 0.8769 (mt) cc_final: 0.8569 (mm) REVERT: C 376 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: C 413 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.7618 (mtp) REVERT: C 423 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7741 (mp0) REVERT: C 436 LYS cc_start: 0.8306 (tmtt) cc_final: 0.7498 (ttmt) REVERT: C 440 ASP cc_start: 0.8505 (t70) cc_final: 0.8279 (t70) REVERT: C 456 MET cc_start: 0.8586 (mtm) cc_final: 0.8235 (mtp) REVERT: C 485 LYS cc_start: 0.7459 (tttt) cc_final: 0.7216 (ptmm) REVERT: C 504 GLU cc_start: 0.7915 (tp30) cc_final: 0.7153 (tp30) REVERT: C 508 ASN cc_start: 0.7839 (t0) cc_final: 0.7505 (m-40) REVERT: D 43 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7710 (ttp-170) REVERT: G 52 TRP cc_start: 0.8965 (OUTLIER) cc_final: 0.8656 (t60) outliers start: 85 outliers final: 64 residues processed: 301 average time/residue: 0.1401 time to fit residues: 64.3844 Evaluate side-chains 287 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 214 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 502 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 65 CYS 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 200 GLU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 376 TYR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 492 PHE Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 52 TRP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 36 TYR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 211 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 426 ASN I 27 GLN K 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.111090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.084558 restraints weight = 22157.299| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.79 r_work: 0.2680 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18024 Z= 0.159 Angle : 0.591 7.678 24529 Z= 0.295 Chirality : 0.045 0.203 2738 Planarity : 0.005 0.084 3103 Dihedral : 8.715 100.251 3084 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 4.70 % Allowed : 18.49 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.36 (0.18), residues: 2132 helix: -0.03 (0.31), residues: 330 sheet: -0.65 (0.22), residues: 606 loop : -1.28 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 92 TYR 0.014 0.001 TYR H 117 PHE 0.017 0.001 PHE D 87 TRP 0.017 0.001 TRP G 52 HIS 0.006 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (17973) covalent geometry : angle 0.56487 / 0.29 (24397) SS BOND : bond 0.00444 / 0.27 ( 21) SS BOND : angle 2.22237 / 1.27 ( 42) hydrogen bonds : bond 0.03065 / 2.03 ( 512) hydrogen bonds : angle 4.97123 / 3.60 ( 1521) link_ALPHA1-3 : bond 0.00764 / 0.38 ( 3) link_ALPHA1-3 : angle 1.65280 / 0.97 ( 9) link_BETA1-2 : bond 0.00128 / 0.06 ( 3) link_BETA1-2 : angle 1.44214 / 1.04 ( 9) link_BETA1-4 : bond 0.00323 / 0.19 ( 9) link_BETA1-4 : angle 2.72985 / 1.76 ( 27) link_BETA2-3 : bond 0.00865 / 0.43 ( 3) link_BETA2-3 : angle 5.18658 / 2.84 ( 9) link_NAG-ASN : bond 0.00262 / 0.17 ( 12) link_NAG-ASN : angle 1.59319 / 1.01 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 222 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7602 (mtm) REVERT: A 106 ASN cc_start: 0.8135 (t0) cc_final: 0.7726 (t0) REVERT: A 146 CYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7872 (m) REVERT: A 312 SER cc_start: 0.8782 (m) cc_final: 0.8545 (t) REVERT: A 373 ASP cc_start: 0.7988 (p0) cc_final: 0.7668 (t0) REVERT: A 411 ASP cc_start: 0.7924 (m-30) cc_final: 0.7704 (t0) REVERT: A 456 MET cc_start: 0.8461 (mtm) cc_final: 0.8180 (mtp) REVERT: A 485 LYS cc_start: 0.8431 (mtpt) cc_final: 0.7845 (ttmm) REVERT: A 510 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8433 (p) REVERT: B 32 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8276 (mmtt) REVERT: B 76 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7789 (mpp) REVERT: B 157 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7461 (mtp180) REVERT: B 183 ARG cc_start: 0.8063 (tpm170) cc_final: 0.7792 (tpp-160) REVERT: B 200 GLU cc_start: 0.8510 (tt0) cc_final: 0.8002 (tt0) REVERT: B 301 LYS cc_start: 0.8483 (mttt) cc_final: 0.8277 (mttm) REVERT: B 371 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8234 (ttp) REVERT: B 437 LYS cc_start: 0.8159 (mmtp) cc_final: 0.7546 (mttt) REVERT: B 440 ASP cc_start: 0.8488 (t0) cc_final: 0.7764 (t70) REVERT: B 460 ARG cc_start: 0.7877 (mtt90) cc_final: 0.7430 (mtp85) REVERT: C 30 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8365 (mmt) REVERT: C 76 MET cc_start: 0.8414 (mmp) cc_final: 0.7553 (mtm) REVERT: C 106 ASN cc_start: 0.8043 (t0) cc_final: 0.7726 (t0) REVERT: C 209 ILE cc_start: 0.8805 (mt) cc_final: 0.8595 (mm) REVERT: C 376 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: C 413 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.7509 (mtp) REVERT: C 416 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8537 (mt0) REVERT: C 423 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7759 (mp0) REVERT: C 436 LYS cc_start: 0.8294 (tmtt) cc_final: 0.7469 (ttmt) REVERT: C 440 ASP cc_start: 0.8528 (t70) cc_final: 0.8318 (t70) REVERT: C 456 MET cc_start: 0.8600 (mtm) cc_final: 0.8267 (mtp) REVERT: C 485 LYS cc_start: 0.7490 (tttt) cc_final: 0.7224 (ptmm) REVERT: C 504 GLU cc_start: 0.7883 (tp30) cc_final: 0.7127 (tp30) REVERT: C 508 ASN cc_start: 0.7832 (t0) cc_final: 0.7516 (m-40) REVERT: D 43 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7785 (ttp-170) REVERT: G 52 TRP cc_start: 0.9039 (OUTLIER) cc_final: 0.8733 (t60) outliers start: 89 outliers final: 71 residues processed: 296 average time/residue: 0.1312 time to fit residues: 59.3329 Evaluate side-chains 297 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 214 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 502 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 65 CYS 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 200 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 376 TYR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 416 GLN Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 52 TRP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 36 TYR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 157 optimal weight: 0.0470 chunk 17 optimal weight: 0.8980 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 426 ASN K 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.111165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.084617 restraints weight = 22095.358| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.78 r_work: 0.2682 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18024 Z= 0.156 Angle : 0.583 7.602 24529 Z= 0.291 Chirality : 0.045 0.195 2738 Planarity : 0.005 0.083 3103 Dihedral : 8.677 98.806 3084 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 4.81 % Allowed : 18.86 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.30 (0.18), residues: 2132 helix: -0.01 (0.30), residues: 333 sheet: -0.59 (0.22), residues: 606 loop : -1.25 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 92 TYR 0.013 0.001 TYR D 117 PHE 0.016 0.001 PHE D 87 TRP 0.017 0.001 TRP G 52 HIS 0.006 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (17973) covalent geometry : angle 0.55865 / 0.28 (24397) SS BOND : bond 0.00384 / 0.24 ( 21) SS BOND : angle 2.02661 / 1.16 ( 42) hydrogen bonds : bond 0.03028 / 2.01 ( 512) hydrogen bonds : angle 4.95512 / 3.59 ( 1521) link_ALPHA1-3 : bond 0.00735 / 0.37 ( 3) link_ALPHA1-3 : angle 1.61179 / 0.97 ( 9) link_BETA1-2 : bond 0.00133 / 0.07 ( 3) link_BETA1-2 : angle 1.36441 / 0.98 ( 9) link_BETA1-4 : bond 0.00308 / 0.18 ( 9) link_BETA1-4 : angle 2.72074 / 1.76 ( 27) link_BETA2-3 : bond 0.00823 / 0.41 ( 3) link_BETA2-3 : angle 5.13394 / 2.82 ( 9) link_NAG-ASN : bond 0.00278 / 0.19 ( 12) link_NAG-ASN : angle 1.53558 / 0.97 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 218 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7584 (mtm) REVERT: A 106 ASN cc_start: 0.8150 (t0) cc_final: 0.7740 (t0) REVERT: A 146 CYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7865 (m) REVERT: A 312 SER cc_start: 0.8746 (m) cc_final: 0.8521 (t) REVERT: A 371 MET cc_start: 0.8539 (ttt) cc_final: 0.8220 (ttt) REVERT: A 373 ASP cc_start: 0.7990 (p0) cc_final: 0.7650 (t0) REVERT: A 411 ASP cc_start: 0.7928 (m-30) cc_final: 0.7689 (t0) REVERT: A 456 MET cc_start: 0.8451 (mtm) cc_final: 0.8189 (mtp) REVERT: A 485 LYS cc_start: 0.8473 (mtpt) cc_final: 0.7909 (ttmm) REVERT: A 510 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8453 (p) REVERT: B 32 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8280 (mmtt) REVERT: B 76 MET cc_start: 0.8434 (mmp) cc_final: 0.7759 (mpp) REVERT: B 157 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7771 (mtp180) REVERT: B 183 ARG cc_start: 0.8043 (tpm170) cc_final: 0.7839 (tpp-160) REVERT: B 200 GLU cc_start: 0.8509 (tt0) cc_final: 0.8001 (tt0) REVERT: B 301 LYS cc_start: 0.8484 (mttt) cc_final: 0.8273 (mttm) REVERT: B 371 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8255 (ttp) REVERT: B 437 LYS cc_start: 0.8144 (mmtp) cc_final: 0.7506 (mttt) REVERT: B 460 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7422 (mtp85) REVERT: C 30 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8353 (mmt) REVERT: C 76 MET cc_start: 0.8410 (mmp) cc_final: 0.7574 (mtm) REVERT: C 106 ASN cc_start: 0.8052 (t0) cc_final: 0.7735 (t0) REVERT: C 209 ILE cc_start: 0.8808 (mt) cc_final: 0.8597 (mm) REVERT: C 376 TYR cc_start: 0.9196 (OUTLIER) cc_final: 0.7743 (m-80) REVERT: C 413 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7495 (mtp) REVERT: C 416 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8531 (mt0) REVERT: C 423 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7775 (mp0) REVERT: C 436 LYS cc_start: 0.8288 (tmtt) cc_final: 0.7458 (ttmt) REVERT: C 456 MET cc_start: 0.8579 (mtm) cc_final: 0.8247 (mtp) REVERT: C 485 LYS cc_start: 0.7479 (tttt) cc_final: 0.7163 (ptmm) REVERT: C 504 GLU cc_start: 0.7888 (tp30) cc_final: 0.7174 (tp30) REVERT: C 508 ASN cc_start: 0.7821 (t0) cc_final: 0.7527 (m-40) REVERT: L 105 MET cc_start: 0.8768 (ttt) cc_final: 0.8542 (ttt) REVERT: D 43 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7775 (ttp-170) REVERT: G 43 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7105 (ttp-170) REVERT: G 52 TRP cc_start: 0.9036 (OUTLIER) cc_final: 0.8722 (t60) outliers start: 91 outliers final: 74 residues processed: 295 average time/residue: 0.1412 time to fit residues: 62.9049 Evaluate side-chains 300 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 214 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 502 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 376 TYR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 416 GLN Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 492 PHE Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 52 TRP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 36 TYR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 193 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 211 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN K 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.112742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.086135 restraints weight = 22065.967| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 1.79 r_work: 0.2706 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18024 Z= 0.117 Angle : 0.556 7.499 24529 Z= 0.277 Chirality : 0.044 0.181 2738 Planarity : 0.005 0.083 3103 Dihedral : 8.481 96.048 3084 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 4.81 % Allowed : 18.81 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.15 (0.18), residues: 2132 helix: 0.18 (0.31), residues: 333 sheet: -0.45 (0.22), residues: 606 loop : -1.20 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 92 TYR 0.013 0.001 TYR D 117 PHE 0.014 0.001 PHE D 87 TRP 0.015 0.001 TRP G 52 HIS 0.005 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (17973) covalent geometry : angle 0.53217 / 0.27 (24397) SS BOND : bond 0.00349 / 0.22 ( 21) SS BOND : angle 1.81545 / 1.04 ( 42) hydrogen bonds : bond 0.02870 / 1.89 ( 512) hydrogen bonds : angle 4.84562 / 3.50 ( 1521) link_ALPHA1-3 : bond 0.00823 / 0.41 ( 3) link_ALPHA1-3 : angle 1.62313 / 0.99 ( 9) link_BETA1-2 : bond 0.00113 / 0.06 ( 3) link_BETA1-2 : angle 1.31097 / 0.91 ( 9) link_BETA1-4 : bond 0.00316 / 0.19 ( 9) link_BETA1-4 : angle 2.70917 / 1.74 ( 27) link_BETA2-3 : bond 0.00743 / 0.37 ( 3) link_BETA2-3 : angle 4.80414 / 2.59 ( 9) link_NAG-ASN : bond 0.00251 / 0.17 ( 12) link_NAG-ASN : angle 1.52452 / 0.97 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 220 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7591 (mtm) REVERT: A 106 ASN cc_start: 0.8166 (t0) cc_final: 0.7768 (t0) REVERT: A 146 CYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7847 (m) REVERT: A 371 MET cc_start: 0.8544 (ttt) cc_final: 0.8283 (ttt) REVERT: A 373 ASP cc_start: 0.7979 (p0) cc_final: 0.7599 (t0) REVERT: A 411 ASP cc_start: 0.7920 (m-30) cc_final: 0.7683 (t0) REVERT: A 485 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7833 (ttmm) REVERT: A 510 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8453 (p) REVERT: B 32 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8263 (mmtt) REVERT: B 76 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7762 (mpp) REVERT: B 157 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7737 (mtp180) REVERT: B 183 ARG cc_start: 0.8034 (tpm170) cc_final: 0.7770 (tpp-160) REVERT: B 200 GLU cc_start: 0.8480 (tt0) cc_final: 0.7931 (tt0) REVERT: B 301 LYS cc_start: 0.8487 (mttt) cc_final: 0.8269 (mttm) REVERT: B 371 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8208 (ttp) REVERT: B 437 LYS cc_start: 0.8172 (mmtp) cc_final: 0.7537 (mttt) REVERT: B 460 ARG cc_start: 0.7828 (mtt90) cc_final: 0.7251 (mmm160) REVERT: C 30 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8367 (mmt) REVERT: C 76 MET cc_start: 0.8382 (mmp) cc_final: 0.7568 (mtm) REVERT: C 106 ASN cc_start: 0.8053 (t0) cc_final: 0.7742 (t0) REVERT: C 209 ILE cc_start: 0.8784 (mt) cc_final: 0.8576 (mm) REVERT: C 376 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: C 413 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7561 (mtp) REVERT: C 423 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7748 (mp0) REVERT: C 436 LYS cc_start: 0.8274 (tmtt) cc_final: 0.7436 (ttmt) REVERT: C 456 MET cc_start: 0.8556 (mtm) cc_final: 0.8224 (mtp) REVERT: C 485 LYS cc_start: 0.7403 (tttt) cc_final: 0.7134 (ptmm) REVERT: C 504 GLU cc_start: 0.7880 (tp30) cc_final: 0.7157 (tp30) REVERT: C 508 ASN cc_start: 0.7816 (t0) cc_final: 0.7524 (m-40) REVERT: L 105 MET cc_start: 0.8740 (ttt) cc_final: 0.8529 (ttt) REVERT: D 43 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7684 (ttp-170) REVERT: G 43 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7173 (ttp-170) REVERT: G 52 TRP cc_start: 0.8999 (OUTLIER) cc_final: 0.8732 (t60) outliers start: 91 outliers final: 71 residues processed: 295 average time/residue: 0.1311 time to fit residues: 58.5777 Evaluate side-chains 297 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 214 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 502 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 467 SER 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 30 MET Chi-restraints excluded: chain C residue 65 CYS 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 200 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 376 TYR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 492 PHE Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 52 TRP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 36 TYR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 17 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 12 optimal weight: 0.1980 chunk 185 optimal weight: 0.0470 chunk 92 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN L 27 GLN K 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.112589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.086051 restraints weight = 21933.096| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.79 r_work: 0.2702 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18024 Z= 0.127 Angle : 0.558 7.343 24529 Z= 0.278 Chirality : 0.044 0.176 2738 Planarity : 0.005 0.083 3103 Dihedral : 8.286 93.782 3080 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.10 % Favored : 93.81 % Rotamer: Outliers : 4.60 % Allowed : 18.96 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.09 (0.18), residues: 2132 helix: 0.26 (0.31), residues: 333 sheet: -0.42 (0.22), residues: 609 loop : -1.16 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 481 TYR 0.013 0.001 TYR D 117 PHE 0.015 0.001 PHE D 87 TRP 0.015 0.001 TRP G 52 HIS 0.004 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (17973) covalent geometry : angle 0.53405 / 0.27 (24397) SS BOND : bond 0.00363 / 0.23 ( 21) SS BOND : angle 1.85329 / 1.07 ( 42) hydrogen bonds : bond 0.02861 / 1.89 ( 512) hydrogen bonds : angle 4.79399 / 3.47 ( 1521) link_ALPHA1-3 : bond 0.00787 / 0.39 ( 3) link_ALPHA1-3 : angle 1.63167 / 1.00 ( 9) link_BETA1-2 : bond 0.00119 / 0.06 ( 3) link_BETA1-2 : angle 1.27201 / 0.88 ( 9) link_BETA1-4 : bond 0.00304 / 0.18 ( 9) link_BETA1-4 : angle 2.69152 / 1.74 ( 27) link_BETA2-3 : bond 0.00757 / 0.38 ( 3) link_BETA2-3 : angle 4.81809 / 2.61 ( 9) link_NAG-ASN : bond 0.00245 / 0.17 ( 12) link_NAG-ASN : angle 1.51368 / 0.96 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 218 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.9128 (p90) cc_final: 0.8896 (p90) REVERT: A 76 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7596 (mtm) REVERT: A 106 ASN cc_start: 0.8167 (t0) cc_final: 0.7773 (t0) REVERT: A 146 CYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7847 (m) REVERT: A 371 MET cc_start: 0.8511 (ttt) cc_final: 0.8258 (ttt) REVERT: A 373 ASP cc_start: 0.7994 (p0) cc_final: 0.7602 (t0) REVERT: A 411 ASP cc_start: 0.7942 (m-30) cc_final: 0.7677 (t0) REVERT: A 485 LYS cc_start: 0.8317 (mtpt) cc_final: 0.7761 (ttmm) REVERT: A 510 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8422 (p) REVERT: B 32 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8292 (mmtt) REVERT: B 76 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7775 (mpp) REVERT: B 157 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7775 (mtp180) REVERT: B 183 ARG cc_start: 0.8051 (tpm170) cc_final: 0.7795 (tpp-160) REVERT: B 200 GLU cc_start: 0.8480 (tt0) cc_final: 0.7946 (tt0) REVERT: B 301 LYS cc_start: 0.8492 (mttt) cc_final: 0.8290 (mttm) REVERT: B 371 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8239 (ttp) REVERT: B 437 LYS cc_start: 0.8125 (mmtp) cc_final: 0.7475 (mttt) REVERT: B 460 ARG cc_start: 0.7853 (mtt90) cc_final: 0.7399 (mtp85) REVERT: C 30 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8372 (mmt) REVERT: C 76 MET cc_start: 0.8406 (mmp) cc_final: 0.7534 (mtm) REVERT: C 106 ASN cc_start: 0.8053 (t0) cc_final: 0.7747 (t0) REVERT: C 209 ILE cc_start: 0.8790 (mt) cc_final: 0.8582 (mm) REVERT: C 376 TYR cc_start: 0.9171 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: C 413 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7563 (mtp) REVERT: C 423 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7754 (mp0) REVERT: C 436 LYS cc_start: 0.8286 (tmtt) cc_final: 0.7450 (ttmt) REVERT: C 456 MET cc_start: 0.8560 (mtm) cc_final: 0.8232 (mtp) REVERT: C 485 LYS cc_start: 0.7421 (tttt) cc_final: 0.7139 (ptmm) REVERT: C 504 GLU cc_start: 0.7882 (tp30) cc_final: 0.7188 (tp30) REVERT: C 508 ASN cc_start: 0.7755 (t0) cc_final: 0.7474 (m-40) REVERT: D 43 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7686 (ttp-170) REVERT: G 43 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7173 (ttp-170) REVERT: G 52 TRP cc_start: 0.9010 (OUTLIER) cc_final: 0.8760 (t60) outliers start: 87 outliers final: 71 residues processed: 289 average time/residue: 0.1434 time to fit residues: 62.5035 Evaluate side-chains 293 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 210 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 502 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 376 TYR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 492 PHE Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 52 TRP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 36 TYR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 TYR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 204 optimal weight: 4.9990 chunk 141 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 206 optimal weight: 0.0030 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 416 GLN L 27 GLN K 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.110698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.084029 restraints weight = 22179.520| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 1.79 r_work: 0.2669 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18024 Z= 0.199 Angle : 0.611 7.541 24529 Z= 0.305 Chirality : 0.046 0.231 2738 Planarity : 0.005 0.084 3103 Dihedral : 8.451 93.528 3080 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.57 % Rotamer: Outliers : 4.49 % Allowed : 18.91 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.09 (0.18), residues: 2132 helix: 0.29 (0.31), residues: 327 sheet: -0.32 (0.22), residues: 579 loop : -1.21 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 481 TYR 0.015 0.001 TYR K 55 PHE 0.019 0.002 PHE D 87 TRP 0.018 0.001 TRP G 52 HIS 0.005 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (17973) covalent geometry : angle 0.58512 / 0.30 (24397) SS BOND : bond 0.00502 / 0.30 ( 21) SS BOND : angle 2.43469 / 1.51 ( 42) hydrogen bonds : bond 0.03095 / 2.06 ( 512) hydrogen bonds : angle 4.94260 / 3.57 ( 1521) link_ALPHA1-3 : bond 0.00681 / 0.34 ( 3) link_ALPHA1-3 : angle 1.69461 / 1.03 ( 9) link_BETA1-2 : bond 0.00130 / 0.07 ( 3) link_BETA1-2 : angle 1.29733 / 0.90 ( 9) link_BETA1-4 : bond 0.00277 / 0.16 ( 9) link_BETA1-4 : angle 2.68474 / 1.74 ( 27) link_BETA2-3 : bond 0.00926 / 0.46 ( 3) link_BETA2-3 : angle 5.22032 / 2.90 ( 9) link_NAG-ASN : bond 0.00317 / 0.19 ( 12) link_NAG-ASN : angle 1.54582 / 0.97 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4284.39 seconds wall clock time: 74 minutes 18.28 seconds (4458.28 seconds total)