Starting phenix.real_space_refine on Sun May 3 02:35:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tr2_41568/05_2026/8tr2_41568.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tr2_41568/05_2026/8tr2_41568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tr2_41568/05_2026/8tr2_41568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tr2_41568/05_2026/8tr2_41568.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tr2_41568/05_2026/8tr2_41568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tr2_41568/05_2026/8tr2_41568.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 54 5.16 5 C 6176 2.51 5 N 1882 2.21 5 O 2024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10140 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5055 Classifications: {'peptide': 745} Incomplete info: {'backbone_only': 210, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 716} Chain breaks: 12 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 893 Unresolved non-hydrogen angles: 1308 Unresolved non-hydrogen dihedrals: 577 Unresolved non-hydrogen chiralities: 299 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'TYR:plan': 9, 'TRP:plan': 4, 'PHE:plan': 16, 'HIS:plan': 2, 'ASN:plan1': 6, 'ARG:plan': 6, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 341 Chain: "B" Number of atoms: 5055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5055 Classifications: {'peptide': 745} Incomplete info: {'backbone_only': 210, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 716} Chain breaks: 12 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 893 Unresolved non-hydrogen angles: 1308 Unresolved non-hydrogen dihedrals: 577 Unresolved non-hydrogen chiralities: 299 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'TYR:plan': 9, 'TRP:plan': 4, 'PHE:plan': 16, 'HIS:plan': 2, 'ASN:plan1': 6, 'ARG:plan': 6, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 341 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {' CA': 2, 'JIX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {' CA': 2, 'JIX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.32, per 1000 atoms: 0.23 Number of scatterers: 10140 At special positions: 0 Unit cell: (92.868, 97.98, 181.476, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 54 16.00 O 2024 8.00 N 1882 7.00 C 6176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 527 " distance=2.03 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 412 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 509 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 509 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 562 " 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 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 546.6 milliseconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 12 sheets defined 47.1% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 65 through 82 Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 110 through 118 removed outlier: 4.772A pdb=" N ALA A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 162 removed outlier: 3.720A pdb=" N LEU A 160 " --> pdb=" O GLN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.632A pdb=" N LEU A 178 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A 180 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 removed outlier: 3.930A pdb=" N LYS A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 223 through 236 removed outlier: 3.825A pdb=" N GLN A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 236 " --> pdb=" O GLN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.619A pdb=" N ARG A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.538A pdb=" N VAL A 316 " --> pdb=" O SER A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 339 removed outlier: 3.753A pdb=" N ASP A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 360 Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 390 through 412 Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.534A pdb=" N ILE A 438 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 577 through 602 removed outlier: 4.199A pdb=" N PHE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 630 removed outlier: 4.059A pdb=" N LEU A 624 " --> pdb=" O PHE A 620 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 665 removed outlier: 3.777A pdb=" N ASN A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.759A pdb=" N LEU A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 759 removed outlier: 3.709A pdb=" N SER A 740 " --> pdb=" O SER A 736 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 753 " --> pdb=" O ILE A 749 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 790 Proline residue: A 787 - end of helix Processing helix chain 'A' and resid 802 through 827 Proline residue: A 821 - end of helix Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 101 through 109 Processing helix chain 'B' and resid 110 through 118 removed outlier: 4.772A pdb=" N ALA B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 162 removed outlier: 3.719A pdb=" N LEU B 160 " --> pdb=" O GLN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.632A pdb=" N LEU B 178 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP B 180 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 203 removed outlier: 3.929A pdb=" N LYS B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 223 through 236 removed outlier: 3.826A pdb=" N GLN B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 265 Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.617A pdb=" N ARG B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.538A pdb=" N VAL B 316 " --> pdb=" O SER B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 339 removed outlier: 3.754A pdb=" N ASP B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 360 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 390 through 412 Processing helix chain 'B' and resid 419 through 423 Processing helix chain 'B' and resid 426 through 433 Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.533A pdb=" N ILE B 438 " --> pdb=" O LEU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 577 through 602 removed outlier: 4.198A pdb=" N PHE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 630 removed outlier: 4.059A pdb=" N LEU B 624 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 625 " --> pdb=" O GLY B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 665 removed outlier: 3.777A pdb=" N ASN B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.759A pdb=" N LEU B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 759 removed outlier: 3.708A pdb=" N SER B 740 " --> pdb=" O SER B 736 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 753 " --> pdb=" O ILE B 749 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 790 Proline residue: B 787 - end of helix Processing helix chain 'B' and resid 802 through 827 Proline residue: B 821 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.354A pdb=" N LEU A 39 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS A 94 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 41 " --> pdb=" O HIS A 94 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU A 96 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY A 43 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL A 40 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ILE A 146 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY A 42 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ILE A 169 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 4.286A pdb=" N ARG A 59 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 246 removed outlier: 7.611A pdb=" N VAL A 213 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA A 244 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR A 215 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LYS A 246 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA A 217 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N VAL A 271 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TRP A 297 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU A 323 " --> pdb=" O TRP A 297 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA A 299 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N LEU A 325 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR A 466 " --> pdb=" O HIS A 485 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N HIS A 485 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A 468 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 440 through 441 removed outlier: 3.598A pdb=" N PHE A 440 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 517 through 520 removed outlier: 3.583A pdb=" N ASN A 520 " --> pdb=" O ILE A 530 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 540 through 542 Processing sheet with id=AA7, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.354A pdb=" N LEU B 39 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS B 94 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU B 41 " --> pdb=" O HIS B 94 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU B 96 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY B 43 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL B 40 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N ILE B 146 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY B 42 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ILE B 169 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 48 through 50 removed outlier: 4.286A pdb=" N ARG B 59 " --> pdb=" O GLU B 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 240 through 246 removed outlier: 7.611A pdb=" N VAL B 213 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 244 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B 215 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LYS B 246 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA B 217 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL B 271 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TRP B 297 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU B 323 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA B 299 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N LEU B 325 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR B 466 " --> pdb=" O HIS B 485 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N HIS B 485 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 468 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 440 through 441 removed outlier: 3.597A pdb=" N PHE B 440 " --> pdb=" O VAL B 454 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 517 through 520 removed outlier: 3.583A pdb=" N ASN B 520 " --> pdb=" O ILE B 530 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 540 through 542 502 hydrogen bonds defined for protein. 1458 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: 1.50 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3626 1.35 - 1.46: 2400 1.46 - 1.58: 4198 1.58 - 1.70: 0 1.70 - 1.81: 76 Bond restraints: 10300 Sorted by residual: bond pdb=" C3 JIX B1001 " pdb=" C5 JIX B1001 " ideal model delta sigma weight residual 1.484 1.554 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C3 JIX A1001 " pdb=" C5 JIX A1001 " ideal model delta sigma weight residual 1.484 1.554 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C5 JIX A1001 " pdb=" O1 JIX A1001 " ideal model delta sigma weight residual 1.400 1.467 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C5 JIX B1001 " pdb=" O1 JIX B1001 " ideal model delta sigma weight residual 1.400 1.467 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1 JIX B1001 " pdb=" O1 JIX B1001 " ideal model delta sigma weight residual 1.423 1.467 -0.044 2.00e-02 2.50e+03 4.77e+00 ... (remaining 10295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 13708 4.49 - 8.99: 18 8.99 - 13.48: 0 13.48 - 17.98: 0 17.98 - 22.47: 4 Bond angle restraints: 13730 Sorted by residual: angle pdb=" C4 JIX A1001 " pdb=" C5 JIX A1001 " pdb=" O1 JIX A1001 " ideal model delta sigma weight residual 118.23 140.70 -22.47 3.00e+00 1.11e-01 5.61e+01 angle pdb=" C4 JIX B1001 " pdb=" C5 JIX B1001 " pdb=" O1 JIX B1001 " ideal model delta sigma weight residual 118.23 140.70 -22.47 3.00e+00 1.11e-01 5.61e+01 angle pdb=" C2 JIX B1001 " pdb=" C3 JIX B1001 " pdb=" C4 JIX B1001 " ideal model delta sigma weight residual 120.55 140.27 -19.72 3.00e+00 1.11e-01 4.32e+01 angle pdb=" C2 JIX A1001 " pdb=" C3 JIX A1001 " pdb=" C4 JIX A1001 " ideal model delta sigma weight residual 120.55 140.26 -19.71 3.00e+00 1.11e-01 4.32e+01 angle pdb=" CA LYS B 254 " pdb=" CB LYS B 254 " pdb=" CG LYS B 254 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 ... (remaining 13725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4955 17.83 - 35.65: 525 35.65 - 53.48: 124 53.48 - 71.30: 20 71.30 - 89.13: 10 Dihedral angle restraints: 5634 sinusoidal: 2152 harmonic: 3482 Sorted by residual: dihedral pdb=" CB CYS A 57 " pdb=" SG CYS A 57 " pdb=" SG CYS A 99 " pdb=" CB CYS A 99 " ideal model delta sinusoidal sigma weight residual 93.00 34.06 58.94 1 1.00e+01 1.00e-02 4.65e+01 dihedral pdb=" CB CYS B 57 " pdb=" SG CYS B 57 " pdb=" SG CYS B 99 " pdb=" CB CYS B 99 " ideal model delta sinusoidal sigma weight residual 93.00 34.06 58.94 1 1.00e+01 1.00e-02 4.65e+01 dihedral pdb=" CB CYS A 361 " pdb=" SG CYS A 361 " pdb=" SG CYS A 373 " pdb=" CB CYS A 373 " ideal model delta sinusoidal sigma weight residual 93.00 137.01 -44.01 1 1.00e+01 1.00e-02 2.70e+01 ... (remaining 5631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1254 0.147 - 0.294: 2 0.294 - 0.441: 2 0.441 - 0.587: 2 0.587 - 0.734: 2 Chirality restraints: 1262 Sorted by residual: chirality pdb=" C3 JIX B1001 " pdb=" C2 JIX B1001 " pdb=" C4 JIX B1001 " pdb=" C5 JIX B1001 " both_signs ideal model delta sigma weight residual True 2.55 -1.82 0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" C3 JIX A1001 " pdb=" C2 JIX A1001 " pdb=" C4 JIX A1001 " pdb=" C5 JIX A1001 " both_signs ideal model delta sigma weight residual True 2.55 -1.82 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C5 JIX B1001 " pdb=" C3 JIX B1001 " pdb=" C4 JIX B1001 " pdb=" O1 JIX B1001 " both_signs ideal model delta sigma weight residual True 2.38 -1.87 0.51 2.00e-01 2.50e+01 6.57e+00 ... (remaining 1259 not shown) Planarity restraints: 1918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 719 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO B 720 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 720 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 720 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 719 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 720 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 720 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 720 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 350 " -0.008 2.00e-02 2.50e+03 6.29e-03 9.90e-01 pdb=" CG TRP B 350 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP B 350 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP B 350 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 350 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 350 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 350 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 350 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 350 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 350 " -0.001 2.00e-02 2.50e+03 ... (remaining 1915 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 238 2.69 - 3.24: 9893 3.24 - 3.80: 14617 3.80 - 4.35: 19950 4.35 - 4.90: 32415 Nonbonded interactions: 77113 Sorted by model distance: nonbonded pdb=" OH TYR B 222 " pdb=" OG SER B 300 " model vdw 2.140 3.040 nonbonded pdb=" OH TYR A 222 " pdb=" OG SER A 300 " model vdw 2.140 3.040 nonbonded pdb=" O ASP B 221 " pdb=" OG1 THR B 225 " model vdw 2.217 3.040 nonbonded pdb=" O ASP A 221 " pdb=" OG1 THR A 225 " model vdw 2.218 3.040 nonbonded pdb=" OD2 ASP B 493 " pdb=" OG SER B 496 " model vdw 2.243 3.040 ... (remaining 77108 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.390 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 0.002 0.070 10314 Z= 0.122 Angle : 0.633 22.475 13758 Z= 0.299 Chirality : 0.056 0.734 1262 Planarity : 0.002 0.031 1918 Dihedral : 14.883 89.127 3620 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.22 % Allowed : 19.60 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.23), residues: 1438 helix: 1.23 (0.21), residues: 606 sheet: -1.65 (0.43), residues: 144 loop : -1.41 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 282 TYR 0.015 0.001 TYR B 539 PHE 0.009 0.001 PHE B 45 TRP 0.017 0.001 TRP B 350 HIS 0.002 0.000 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00242 (10300) covalent geometry : angle 0.63315 (13730) SS BOND : bond 0.00190 ( 14) SS BOND : angle 0.68807 ( 28) hydrogen bonds : bond 0.27709 ( 502) hydrogen bonds : angle 6.91543 ( 1458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.318 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 46 average time/residue: 0.0766 time to fit residues: 5.8659 Evaluate side-chains 46 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 CYS Chi-restraints excluded: chain B residue 562 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 55 optimal weight: 30.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.111708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.073234 restraints weight = 22891.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.073891 restraints weight = 16051.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.075215 restraints weight = 12304.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.075160 restraints weight = 12351.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.074992 restraints weight = 9314.316| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10314 Z= 0.161 Angle : 0.510 7.366 13758 Z= 0.281 Chirality : 0.043 0.127 1262 Planarity : 0.003 0.030 1918 Dihedral : 4.615 37.067 1628 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.54 % Allowed : 17.51 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.22), residues: 1438 helix: 1.44 (0.21), residues: 626 sheet: -1.37 (0.45), residues: 136 loop : -1.47 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 282 TYR 0.013 0.001 TYR A 539 PHE 0.014 0.001 PHE B 275 TRP 0.011 0.001 TRP B 355 HIS 0.002 0.000 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00348 (10300) covalent geometry : angle 0.50902 (13730) SS BOND : bond 0.00255 ( 14) SS BOND : angle 0.94200 ( 28) hydrogen bonds : bond 0.05825 ( 502) hydrogen bonds : angle 4.62468 ( 1458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 60 average time/residue: 0.0777 time to fit residues: 7.5260 Evaluate side-chains 57 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 562 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 549 CYS Chi-restraints excluded: chain B residue 562 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 63 optimal weight: 8.9990 chunk 135 optimal weight: 50.0000 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.0040 chunk 7 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 117 optimal weight: 0.0470 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.114465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.071415 restraints weight = 22493.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.073830 restraints weight = 12680.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.075390 restraints weight = 9217.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.075998 restraints weight = 7615.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.076834 restraints weight = 6929.735| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10314 Z= 0.099 Angle : 0.434 6.324 13758 Z= 0.237 Chirality : 0.041 0.132 1262 Planarity : 0.002 0.030 1918 Dihedral : 4.241 39.056 1628 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.31 % Favored : 95.55 % Rotamer: Outliers : 2.97 % Allowed : 15.86 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.23), residues: 1438 helix: 1.65 (0.21), residues: 618 sheet: -0.87 (0.44), residues: 144 loop : -1.41 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 282 TYR 0.011 0.001 TYR B 539 PHE 0.010 0.001 PHE B 275 TRP 0.010 0.001 TRP A 355 HIS 0.001 0.000 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00193 (10300) covalent geometry : angle 0.43242 (13730) SS BOND : bond 0.00457 ( 14) SS BOND : angle 0.88845 ( 28) hydrogen bonds : bond 0.04576 ( 502) hydrogen bonds : angle 4.12959 ( 1458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 45 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 PHE cc_start: 0.7976 (m-80) cc_final: 0.7773 (m-80) REVERT: B 547 MET cc_start: 0.7258 (ppp) cc_final: 0.6501 (ppp) outliers start: 27 outliers final: 17 residues processed: 70 average time/residue: 0.0675 time to fit residues: 8.0752 Evaluate side-chains 62 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 562 CYS Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 549 CYS Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 563 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 116 optimal weight: 2.9990 chunk 60 optimal weight: 0.0870 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 95 optimal weight: 0.2980 chunk 115 optimal weight: 1.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.113691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.070374 restraints weight = 22741.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.072762 restraints weight = 12994.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.074247 restraints weight = 9477.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.075198 restraints weight = 7880.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.075716 restraints weight = 7006.177| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10314 Z= 0.119 Angle : 0.435 6.538 13758 Z= 0.237 Chirality : 0.041 0.134 1262 Planarity : 0.002 0.031 1918 Dihedral : 4.233 38.721 1628 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.52 % Favored : 95.34 % Rotamer: Outliers : 2.42 % Allowed : 16.19 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.23), residues: 1438 helix: 1.85 (0.21), residues: 614 sheet: -0.84 (0.44), residues: 144 loop : -1.36 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 282 TYR 0.010 0.001 TYR B 171 PHE 0.010 0.001 PHE A 275 TRP 0.009 0.001 TRP B 355 HIS 0.002 0.000 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00256 (10300) covalent geometry : angle 0.43325 (13730) SS BOND : bond 0.00239 ( 14) SS BOND : angle 0.89173 ( 28) hydrogen bonds : bond 0.04477 ( 502) hydrogen bonds : angle 3.94124 ( 1458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: A 407 MET cc_start: 0.8684 (tpp) cc_final: 0.8482 (ttm) REVERT: B 387 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: B 407 MET cc_start: 0.8683 (tpp) cc_final: 0.8461 (ttm) REVERT: B 547 MET cc_start: 0.7263 (ppp) cc_final: 0.6446 (ppp) REVERT: B 558 ASP cc_start: 0.8360 (p0) cc_final: 0.8124 (p0) outliers start: 22 outliers final: 16 residues processed: 68 average time/residue: 0.0645 time to fit residues: 7.6319 Evaluate side-chains 64 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 562 CYS Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 549 CYS Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 563 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 142 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 131 optimal weight: 40.0000 chunk 63 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.111591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.068253 restraints weight = 22735.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.070458 restraints weight = 13115.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.071926 restraints weight = 9704.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.072809 restraints weight = 8104.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.073246 restraints weight = 7248.376| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10314 Z= 0.232 Angle : 0.517 8.329 13758 Z= 0.280 Chirality : 0.045 0.125 1262 Planarity : 0.003 0.029 1918 Dihedral : 4.538 38.293 1628 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.20 % Allowed : 17.18 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.23), residues: 1438 helix: 1.74 (0.21), residues: 622 sheet: -1.02 (0.44), residues: 140 loop : -1.35 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.013 0.001 TYR A 171 PHE 0.018 0.002 PHE A 295 TRP 0.013 0.002 TRP B 303 HIS 0.003 0.001 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00538 (10300) covalent geometry : angle 0.51598 (13730) SS BOND : bond 0.00278 ( 14) SS BOND : angle 0.87280 ( 28) hydrogen bonds : bond 0.05142 ( 502) hydrogen bonds : angle 3.99297 ( 1458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 547 MET cc_start: 0.7266 (ppp) cc_final: 0.6528 (ppp) outliers start: 20 outliers final: 16 residues processed: 64 average time/residue: 0.0623 time to fit residues: 6.9969 Evaluate side-chains 60 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 562 CYS Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 549 CYS Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 563 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 116 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 14 optimal weight: 0.2980 chunk 103 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.113835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.070963 restraints weight = 22621.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.073289 restraints weight = 13073.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.074782 restraints weight = 9574.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.075748 restraints weight = 7917.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.076214 restraints weight = 7035.568| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10314 Z= 0.098 Angle : 0.429 8.226 13758 Z= 0.233 Chirality : 0.041 0.125 1262 Planarity : 0.002 0.029 1918 Dihedral : 4.222 40.547 1628 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.09 % Allowed : 17.73 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1438 helix: 1.90 (0.21), residues: 620 sheet: -0.86 (0.44), residues: 140 loop : -1.43 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 282 TYR 0.010 0.001 TYR A 539 PHE 0.009 0.001 PHE B 275 TRP 0.009 0.001 TRP A 350 HIS 0.002 0.000 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00200 (10300) covalent geometry : angle 0.42765 (13730) SS BOND : bond 0.00230 ( 14) SS BOND : angle 0.82038 ( 28) hydrogen bonds : bond 0.04085 ( 502) hydrogen bonds : angle 3.76578 ( 1458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: B 387 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8424 (tt0) REVERT: B 547 MET cc_start: 0.7225 (ppp) cc_final: 0.6494 (ppp) REVERT: B 558 ASP cc_start: 0.8352 (p0) cc_final: 0.7942 (t0) outliers start: 19 outliers final: 14 residues processed: 66 average time/residue: 0.0644 time to fit residues: 7.3729 Evaluate side-chains 62 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 562 CYS Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 549 CYS Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 563 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.0020 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 121 optimal weight: 0.0980 chunk 141 optimal weight: 50.0000 chunk 55 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.113767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.070556 restraints weight = 22478.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.072871 restraints weight = 13130.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.074271 restraints weight = 9671.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.075255 restraints weight = 8076.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.075718 restraints weight = 7172.174| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10314 Z= 0.111 Angle : 0.434 9.251 13758 Z= 0.235 Chirality : 0.041 0.124 1262 Planarity : 0.002 0.029 1918 Dihedral : 4.187 40.268 1628 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.20 % Allowed : 17.73 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.23), residues: 1438 helix: 1.98 (0.21), residues: 628 sheet: -0.71 (0.43), residues: 144 loop : -1.43 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 270 TYR 0.010 0.001 TYR A 171 PHE 0.011 0.001 PHE A 275 TRP 0.011 0.001 TRP A 297 HIS 0.001 0.000 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00240 (10300) covalent geometry : angle 0.43308 (13730) SS BOND : bond 0.00288 ( 14) SS BOND : angle 0.82819 ( 28) hydrogen bonds : bond 0.04091 ( 502) hydrogen bonds : angle 3.65751 ( 1458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8420 (tt0) REVERT: B 387 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8424 (tt0) REVERT: B 547 MET cc_start: 0.7240 (ppp) cc_final: 0.6458 (ppp) REVERT: B 558 ASP cc_start: 0.8335 (p0) cc_final: 0.7928 (t0) outliers start: 20 outliers final: 17 residues processed: 65 average time/residue: 0.0643 time to fit residues: 7.2992 Evaluate side-chains 66 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 562 CYS Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 549 CYS Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 563 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 3 optimal weight: 2.9990 chunk 117 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 61 optimal weight: 50.0000 chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 50.0000 chunk 71 optimal weight: 8.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.111323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.067936 restraints weight = 22683.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.070056 restraints weight = 13734.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.071389 restraints weight = 10304.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.072255 restraints weight = 8649.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.072683 restraints weight = 7768.755| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10314 Z= 0.267 Angle : 0.548 9.518 13758 Z= 0.295 Chirality : 0.046 0.126 1262 Planarity : 0.003 0.028 1918 Dihedral : 4.639 40.218 1628 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.31 % Allowed : 17.73 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.23), residues: 1438 helix: 1.82 (0.21), residues: 634 sheet: -1.17 (0.42), residues: 148 loop : -1.46 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 68 TYR 0.014 0.002 TYR A 171 PHE 0.020 0.002 PHE A 295 TRP 0.012 0.002 TRP B 303 HIS 0.003 0.001 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00626 (10300) covalent geometry : angle 0.54710 (13730) SS BOND : bond 0.00292 ( 14) SS BOND : angle 0.90952 ( 28) hydrogen bonds : bond 0.05111 ( 502) hydrogen bonds : angle 3.84480 ( 1458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8523 (tt0) REVERT: B 387 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: B 547 MET cc_start: 0.7284 (ppp) cc_final: 0.6576 (ppp) outliers start: 21 outliers final: 18 residues processed: 65 average time/residue: 0.0639 time to fit residues: 7.2332 Evaluate side-chains 66 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 562 CYS Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 549 CYS Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 563 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 125 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 0.0270 chunk 5 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.113894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.070828 restraints weight = 22457.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.073012 restraints weight = 13395.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.074486 restraints weight = 9983.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.075400 restraints weight = 8342.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.075722 restraints weight = 7447.526| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10314 Z= 0.101 Angle : 0.429 5.401 13758 Z= 0.234 Chirality : 0.041 0.125 1262 Planarity : 0.002 0.028 1918 Dihedral : 4.235 42.657 1628 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.09 % Allowed : 17.84 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1438 helix: 1.96 (0.21), residues: 634 sheet: -0.75 (0.43), residues: 140 loop : -1.60 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 282 TYR 0.009 0.001 TYR A 539 PHE 0.010 0.001 PHE A 275 TRP 0.009 0.001 TRP A 297 HIS 0.002 0.000 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00215 (10300) covalent geometry : angle 0.42740 (13730) SS BOND : bond 0.00248 ( 14) SS BOND : angle 0.81137 ( 28) hydrogen bonds : bond 0.03929 ( 502) hydrogen bonds : angle 3.61807 ( 1458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8433 (tt0) REVERT: A 539 TYR cc_start: 0.8182 (p90) cc_final: 0.7838 (p90) REVERT: B 387 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8436 (tt0) REVERT: B 547 MET cc_start: 0.7217 (ppp) cc_final: 0.6523 (ppp) REVERT: B 558 ASP cc_start: 0.8302 (p0) cc_final: 0.7885 (t0) outliers start: 19 outliers final: 17 residues processed: 67 average time/residue: 0.0685 time to fit residues: 7.8230 Evaluate side-chains 67 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 562 CYS Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 549 CYS Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 563 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 61 optimal weight: 50.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 386 GLN B 357 GLN B 386 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.110620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.067226 restraints weight = 22634.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.069287 restraints weight = 13866.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.070592 restraints weight = 10450.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.071420 restraints weight = 8812.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.071874 restraints weight = 7941.070| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 10314 Z= 0.339 Angle : 0.604 9.875 13758 Z= 0.323 Chirality : 0.048 0.137 1262 Planarity : 0.003 0.030 1918 Dihedral : 4.811 41.189 1628 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.20 % Allowed : 17.40 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.23), residues: 1438 helix: 1.84 (0.21), residues: 628 sheet: -1.19 (0.41), residues: 152 loop : -1.47 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.013 0.002 TYR B 171 PHE 0.023 0.002 PHE B 295 TRP 0.015 0.002 TRP B 303 HIS 0.005 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00795 (10300) covalent geometry : angle 0.60338 (13730) SS BOND : bond 0.00343 ( 14) SS BOND : angle 0.99820 ( 28) hydrogen bonds : bond 0.05415 ( 502) hydrogen bonds : angle 3.89043 ( 1458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 547 MET cc_start: 0.7274 (ppp) cc_final: 0.6594 (ppp) outliers start: 20 outliers final: 20 residues processed: 64 average time/residue: 0.0633 time to fit residues: 7.1107 Evaluate side-chains 66 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain A residue 562 CYS Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 549 CYS Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 563 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 43 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 133 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 GLN B 386 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.113035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.069589 restraints weight = 22539.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.071845 restraints weight = 13321.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.073279 restraints weight = 9854.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.074179 restraints weight = 8243.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.074680 restraints weight = 7362.532| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10314 Z= 0.134 Angle : 0.465 9.888 13758 Z= 0.250 Chirality : 0.042 0.125 1262 Planarity : 0.002 0.028 1918 Dihedral : 4.418 43.537 1628 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.76 % Allowed : 18.17 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.23), residues: 1438 helix: 1.90 (0.21), residues: 632 sheet: -1.04 (0.43), residues: 136 loop : -1.62 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 282 TYR 0.010 0.001 TYR B 171 PHE 0.013 0.001 PHE B 275 TRP 0.010 0.001 TRP A 297 HIS 0.002 0.000 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00303 (10300) covalent geometry : angle 0.46364 (13730) SS BOND : bond 0.00243 ( 14) SS BOND : angle 0.85269 ( 28) hydrogen bonds : bond 0.04214 ( 502) hydrogen bonds : angle 3.66581 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1848.36 seconds wall clock time: 32 minutes 32.42 seconds (1952.42 seconds total)