Starting phenix.real_space_refine on Thu Jul 2 20:30:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tr2_41568/07_2026/8tr2_41568.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tr2_41568/07_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_41568/07_2026/8tr2_41568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tr2_41568/07_2026/8tr2_41568.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tr2_41568/07_2026/8tr2_41568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tr2_41568/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 13 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'JIX': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'JIX': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 1.93, per 1000 atoms: 0.19 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: 0.91 Conformation dependent library (CDL) restraints added in 386.4 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: 0.27 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: 1.34 Time building geometry restraints manager: 1.16 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: 7.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.560 Find NCS groups from input model: 0.090 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 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/Z covalent geometry : bond 0.00242 / 0.12 (10300) covalent geometry : angle 0.63315 / 0.30 (13730) SS BOND : bond 0.00190 / 0.12 ( 14) SS BOND : angle 0.68807 / 0.46 ( 28) hydrogen bonds : bond 0.27709 / 18.53 ( 502) hydrogen bonds : angle 6.91543 / 4.76 ( 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 : 0.401 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 46 average time/residue: 0.0666 time to fit residues: 5.1404 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 : 0.381 ------------------------------------------------------------------------------- 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: 0.7980 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: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.111631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.070265 restraints weight = 22916.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.072314 restraints weight = 14258.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.073630 restraints weight = 10826.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.074349 restraints weight = 9127.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.074955 restraints weight = 8253.355| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10314 Z= 0.157 Angle : 0.507 7.361 13758 Z= 0.280 Chirality : 0.043 0.143 1262 Planarity : 0.003 0.030 1918 Dihedral : 4.578 37.149 1628 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.87 % Allowed : 17.18 % 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: -0.19 (0.22), residues: 1438 helix: 1.46 (0.20), residues: 628 sheet: -1.36 (0.45), residues: 136 loop : -1.44 (0.24), residues: 674 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 0.012 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/Z covalent geometry : bond 0.00338 / 0.16 (10300) covalent geometry : angle 0.50622 / 0.28 (13730) SS BOND : bond 0.00261 / 0.17 ( 14) SS BOND : angle 0.94312 / 0.62 ( 28) hydrogen bonds : bond 0.06374 / 4.35 ( 502) hydrogen bonds : angle 4.69142 / 3.18 ( 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 63 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 62 average time/residue: 0.0735 time to fit residues: 7.1837 Evaluate side-chains 56 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 135 optimal weight: 50.0000 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 95 optimal weight: 0.0870 chunk 117 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.114349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.071316 restraints weight = 22514.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.073734 restraints weight = 12755.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.075302 restraints weight = 9257.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.076258 restraints weight = 7638.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.076831 restraints weight = 6808.309| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1529 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= 0.102 Angle : 0.441 6.727 13758 Z= 0.240 Chirality : 0.041 0.137 1262 Planarity : 0.003 0.030 1918 Dihedral : 4.239 39.028 1628 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.24 % Favored : 95.62 % Rotamer: Outliers : 2.75 % Allowed : 15.86 % 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: 0.01 (0.23), residues: 1438 helix: 1.67 (0.21), residues: 618 sheet: -0.83 (0.44), residues: 144 loop : -1.42 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 282 TYR 0.011 0.001 TYR A 539 PHE 0.011 0.001 PHE B 275 TRP 0.011 0.001 TRP B 355 HIS 0.001 0.000 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (10300) covalent geometry : angle 0.43920 / 0.24 (13730) SS BOND : bond 0.00245 / 0.15 ( 14) SS BOND : angle 0.89417 / 0.60 ( 28) hydrogen bonds : bond 0.04582 / 3.11 ( 502) hydrogen bonds : angle 4.10417 / 2.77 ( 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 69 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 547 MET cc_start: 0.7267 (ppp) cc_final: 0.6463 (ppp) outliers start: 25 outliers final: 17 residues processed: 68 average time/residue: 0.0581 time to fit residues: 6.8833 Evaluate side-chains 61 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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: 0.0020 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 102 optimal weight: 0.0000 chunk 71 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.112634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.069123 restraints weight = 22888.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.071460 restraints weight = 13084.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.072965 restraints weight = 9547.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.073781 restraints weight = 7912.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074002 restraints weight = 7128.139| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10314 Z= 0.164 Angle : 0.468 6.050 13758 Z= 0.256 Chirality : 0.043 0.123 1262 Planarity : 0.003 0.030 1918 Dihedral : 4.386 38.303 1628 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.01 % Favored : 94.85 % Rotamer: Outliers : 2.20 % Allowed : 16.74 % Favored : 81.06 % 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: 1.73 (0.21), residues: 620 sheet: -1.03 (0.45), residues: 140 loop : -1.34 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 282 TYR 0.012 0.001 TYR A 171 PHE 0.013 0.001 PHE B 295 TRP 0.010 0.001 TRP B 303 HIS 0.002 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (10300) covalent geometry : angle 0.46678 / 0.26 (13730) SS BOND : bond 0.00242 / 0.15 ( 14) SS BOND : angle 0.90962 / 0.59 ( 28) hydrogen bonds : bond 0.04911 / 3.34 ( 502) hydrogen bonds : angle 4.00303 / 2.71 ( 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 64 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: B 387 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: B 547 MET cc_start: 0.7321 (ppp) cc_final: 0.6433 (ppp) outliers start: 20 outliers final: 16 residues processed: 64 average time/residue: 0.0512 time to fit residues: 5.7904 Evaluate side-chains 62 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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: 1.9990 chunk 125 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 131 optimal weight: 40.0000 chunk 63 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.112827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.069655 restraints weight = 22536.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.071912 restraints weight = 12946.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.073425 restraints weight = 9509.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.074268 restraints weight = 7894.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.074268 restraints weight = 7081.296| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10314 Z= 0.153 Angle : 0.458 7.486 13758 Z= 0.249 Chirality : 0.042 0.125 1262 Planarity : 0.003 0.029 1918 Dihedral : 4.331 39.256 1628 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.75 % Allowed : 16.41 % Favored : 80.84 % 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: 1.82 (0.21), residues: 618 sheet: -0.88 (0.44), residues: 140 loop : -1.35 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 282 TYR 0.013 0.001 TYR A 537 PHE 0.013 0.001 PHE B 295 TRP 0.010 0.001 TRP B 297 HIS 0.002 0.000 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (10300) covalent geometry : angle 0.45723 / 0.25 (13730) SS BOND : bond 0.00260 / 0.16 ( 14) SS BOND : angle 0.83634 / 0.55 ( 28) hydrogen bonds : bond 0.04572 / 3.10 ( 502) hydrogen bonds : angle 3.87029 / 2.61 ( 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 70 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8436 (tt0) REVERT: B 387 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: B 547 MET cc_start: 0.7270 (ppp) cc_final: 0.6506 (ppp) outliers start: 25 outliers final: 17 residues processed: 70 average time/residue: 0.0480 time to fit residues: 5.7764 Evaluate side-chains 64 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 116 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 0.0040 chunk 103 optimal weight: 0.0980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.114469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.071638 restraints weight = 22632.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.074015 restraints weight = 13008.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.075557 restraints weight = 9481.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.076517 restraints weight = 7810.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.077146 restraints weight = 6925.705| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10314 Z= 0.088 Angle : 0.418 8.238 13758 Z= 0.227 Chirality : 0.041 0.128 1262 Planarity : 0.002 0.029 1918 Dihedral : 4.123 40.613 1628 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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: 0.28 (0.23), residues: 1438 helix: 1.99 (0.21), residues: 622 sheet: -0.63 (0.44), residues: 144 loop : -1.43 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 282 TYR 0.010 0.001 TYR B 539 PHE 0.009 0.001 PHE A 275 TRP 0.010 0.001 TRP B 297 HIS 0.001 0.000 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.09 (10300) covalent geometry : angle 0.41705 / 0.23 (13730) SS BOND : bond 0.00368 / 0.23 ( 14) SS BOND : angle 0.84107 / 0.57 ( 28) hydrogen bonds : bond 0.03886 / 2.62 ( 502) hydrogen bonds : angle 3.66975 / 2.48 ( 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 64 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6413 (mp0) REVERT: A 387 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: B 387 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: B 547 MET cc_start: 0.7195 (ppp) cc_final: 0.6401 (ppp) REVERT: B 558 ASP cc_start: 0.8304 (p0) cc_final: 0.7893 (t0) outliers start: 19 outliers final: 14 residues processed: 64 average time/residue: 0.0569 time to fit residues: 6.1835 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 : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 224 GLU 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: 0.0980 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 141 optimal weight: 50.0000 chunk 55 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3784 r_free = 0.3784 target = 0.111235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.067836 restraints weight = 22765.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.069914 restraints weight = 13632.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.071287 restraints weight = 10222.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.072107 restraints weight = 8593.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.072683 restraints weight = 7717.259| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 10314 Z= 0.286 Angle : 0.554 8.906 13758 Z= 0.298 Chirality : 0.046 0.128 1262 Planarity : 0.003 0.030 1918 Dihedral : 4.627 39.399 1628 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.87 % Allowed : 17.95 % 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: 0.18 (0.23), residues: 1438 helix: 1.86 (0.21), residues: 624 sheet: -1.00 (0.42), residues: 152 loop : -1.36 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 68 TYR 0.013 0.002 TYR A 171 PHE 0.020 0.002 PHE A 295 TRP 0.014 0.002 TRP B 303 HIS 0.003 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.29 (10300) covalent geometry : angle 0.55342 / 0.30 (13730) SS BOND : bond 0.00333 / 0.21 ( 14) SS BOND : angle 0.91877 / 0.58 ( 28) hydrogen bonds : bond 0.05211 / 3.54 ( 502) hydrogen bonds : angle 3.88379 / 2.62 ( 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 62 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 PHE cc_start: 0.7934 (m-80) cc_final: 0.7706 (m-80) REVERT: B 547 MET cc_start: 0.7286 (ppp) cc_final: 0.6581 (ppp) outliers start: 17 outliers final: 17 residues processed: 62 average time/residue: 0.0541 time to fit residues: 5.7308 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 : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 224 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 3 optimal weight: 0.9980 chunk 117 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 61 optimal weight: 50.0000 chunk 33 optimal weight: 0.7980 chunk 67 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.113736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.070508 restraints weight = 22424.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.072767 restraints weight = 13332.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074094 restraints weight = 9862.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.075058 restraints weight = 8282.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.075611 restraints weight = 7424.703| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10314 Z= 0.106 Angle : 0.440 9.960 13758 Z= 0.238 Chirality : 0.042 0.124 1262 Planarity : 0.002 0.029 1918 Dihedral : 4.260 41.286 1628 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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: 0.27 (0.23), residues: 1438 helix: 2.02 (0.21), residues: 620 sheet: -0.89 (0.43), residues: 140 loop : -1.40 (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 B 171 PHE 0.010 0.001 PHE A 275 TRP 0.010 0.001 TRP B 297 HIS 0.001 0.000 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (10300) covalent geometry : angle 0.43903 / 0.24 (13730) SS BOND : bond 0.00234 / 0.15 ( 14) SS BOND : angle 0.82739 / 0.55 ( 28) hydrogen bonds : bond 0.04068 / 2.75 ( 502) hydrogen bonds : angle 3.65929 / 2.46 ( 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 63 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: A 387 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: A 544 PHE cc_start: 0.7906 (m-80) cc_final: 0.7683 (m-80) REVERT: B 387 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: B 547 MET cc_start: 0.7222 (ppp) cc_final: 0.6456 (ppp) outliers start: 19 outliers final: 14 residues processed: 63 average time/residue: 0.0538 time to fit residues: 5.9746 Evaluate side-chains 61 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 224 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 125 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.112350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.069108 restraints weight = 22545.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.071328 restraints weight = 13323.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.072770 restraints weight = 9845.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.073567 restraints weight = 8238.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.074172 restraints weight = 7402.614| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 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 : 0.004 0.041 10314 Z= 0.184 Angle : 0.471 5.618 13758 Z= 0.255 Chirality : 0.043 0.124 1262 Planarity : 0.003 0.028 1918 Dihedral : 4.377 41.595 1628 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.87 % Allowed : 17.73 % 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: 0.30 (0.23), residues: 1438 helix: 2.03 (0.21), residues: 620 sheet: -0.96 (0.42), residues: 140 loop : -1.36 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 253 TYR 0.010 0.001 TYR A 171 PHE 0.015 0.001 PHE A 295 TRP 0.011 0.001 TRP A 297 HIS 0.003 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (10300) covalent geometry : angle 0.46971 / 0.25 (13730) SS BOND : bond 0.00247 / 0.16 ( 14) SS BOND : angle 0.81607 / 0.53 ( 28) hydrogen bonds : bond 0.04486 / 3.04 ( 502) hydrogen bonds : angle 3.69969 / 2.49 ( 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 62 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: A 544 PHE cc_start: 0.7936 (m-80) cc_final: 0.7722 (m-80) REVERT: B 387 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8486 (tt0) REVERT: B 547 MET cc_start: 0.7224 (ppp) cc_final: 0.6493 (ppp) outliers start: 17 outliers final: 15 residues processed: 62 average time/residue: 0.0612 time to fit residues: 6.6100 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 : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 224 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 61 optimal weight: 50.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 GLN B 357 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.111162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.067670 restraints weight = 22547.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.069727 restraints weight = 13614.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.071119 restraints weight = 10253.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.071976 restraints weight = 8601.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.072423 restraints weight = 7751.590| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 10314 Z= 0.286 Angle : 0.565 10.637 13758 Z= 0.302 Chirality : 0.046 0.126 1262 Planarity : 0.003 0.028 1918 Dihedral : 4.680 41.521 1628 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % 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: 0.14 (0.23), residues: 1438 helix: 1.89 (0.21), residues: 622 sheet: -1.09 (0.41), residues: 152 loop : -1.43 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.012 0.002 TYR A 171 PHE 0.021 0.002 PHE B 295 TRP 0.014 0.002 TRP B 303 HIS 0.004 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.29 (10300) covalent geometry : angle 0.56430 / 0.30 (13730) SS BOND : bond 0.00315 / 0.20 ( 14) SS BOND : angle 0.94071 / 0.59 ( 28) hydrogen bonds : bond 0.05130 / 3.49 ( 502) hydrogen bonds : angle 3.83947 / 2.58 ( 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 64 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: A 544 PHE cc_start: 0.7968 (m-80) cc_final: 0.7757 (m-80) REVERT: B 547 MET cc_start: 0.7223 (ppp) cc_final: 0.6525 (ppp) outliers start: 19 outliers final: 17 residues processed: 64 average time/residue: 0.0569 time to fit residues: 6.3637 Evaluate side-chains 63 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 301 ASP 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 301 ASP 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: 9.9990 chunk 2 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 133 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.113279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.069878 restraints weight = 22528.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.072102 restraints weight = 13478.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.073541 restraints weight = 10029.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.074416 restraints weight = 8359.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.074969 restraints weight = 7516.418| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10314 Z= 0.134 Angle : 0.460 9.557 13758 Z= 0.248 Chirality : 0.042 0.126 1262 Planarity : 0.002 0.028 1918 Dihedral : 4.371 43.238 1628 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.31 % Allowed : 17.84 % Favored : 79.85 % 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: 1.85 (0.21), residues: 634 sheet: -1.00 (0.43), residues: 136 loop : -1.57 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 253 TYR 0.010 0.001 TYR A 171 PHE 0.012 0.001 PHE A 275 TRP 0.010 0.001 TRP B 297 HIS 0.002 0.000 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (10300) covalent geometry : angle 0.45850 / 0.25 (13730) SS BOND : bond 0.00255 / 0.17 ( 14) SS BOND : angle 0.82386 / 0.54 ( 28) hydrogen bonds : bond 0.04166 / 2.82 ( 502) hydrogen bonds : angle 3.65247 / 2.45 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1617.35 seconds wall clock time: 28 minutes 34.76 seconds (1714.76 seconds total)