Starting phenix.real_space_refine on Mon Oct 26 12:02:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdm_61396/10_2026/9jdm_61396.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdm_61396/10_2026/9jdm_61396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jdm_61396/10_2026/9jdm_61396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdm_61396/10_2026/9jdm_61396.map" model { file = "/net/cci-nas-00/data/ceres_data/9jdm_61396/10_2026/9jdm_61396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdm_61396/10_2026/9jdm_61396.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 124 5.16 5 C 13824 2.51 5 N 3264 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20992 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4946 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 595} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4946 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 595} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 302 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 302 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: B, D Time building chain proxies: 8.77, per 1000 atoms: 0.42 Number of scatterers: 20992 At special positions: 0 Unit cell: (142.31, 142.31, 129.47, 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) S 124 16.00 P 28 15.00 O 3752 8.00 N 3264 7.00 C 13824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " 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: 1.84 Conformation dependent library (CDL) restraints added in 851.6 milliseconds 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4656 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 61.4% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.976A pdb=" N VAL A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.700A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.646A pdb=" N ALA A 175 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.507A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.923A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.684A pdb=" N LEU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.545A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 483 through 507 removed outlier: 4.019A pdb=" N ARG A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 507 " --> pdb=" O ILE A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.942A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 562 Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 606 Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 650 through 667 Processing helix chain 'A' and resid 668 through 687 removed outlier: 3.509A pdb=" N GLY A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 707 Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.975A pdb=" N VAL D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 146 removed outlier: 3.700A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.646A pdb=" N ALA D 175 " --> pdb=" O CYS D 171 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU D 177 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 Processing helix chain 'D' and resid 200 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.506A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.924A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 402 through 410 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.684A pdb=" N LEU D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.545A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 483 through 507 removed outlier: 4.020A pdb=" N ARG D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 507 " --> pdb=" O ILE D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.942A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 562 Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 586 through 606 Processing helix chain 'D' and resid 607 through 609 No H-bonds generated for 'chain 'D' and resid 607 through 609' Processing helix chain 'D' and resid 624 through 637 Processing helix chain 'D' and resid 650 through 667 Processing helix chain 'D' and resid 668 through 687 removed outlier: 3.509A pdb=" N GLY D 678 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 707 Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.976A pdb=" N VAL B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 removed outlier: 3.700A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.646A pdb=" N ALA B 175 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 177 " --> pdb=" O MET B 173 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.507A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.923A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.684A pdb=" N LEU B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.546A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 483 through 507 removed outlier: 4.019A pdb=" N ARG B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 507 " --> pdb=" O ILE B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.942A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 562 Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 606 Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 624 through 637 Processing helix chain 'B' and resid 650 through 667 Processing helix chain 'B' and resid 668 through 687 removed outlier: 3.509A pdb=" N GLY B 678 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 707 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.976A pdb=" N VAL C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.700A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.646A pdb=" N ALA C 175 " --> pdb=" O CYS C 171 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU C 177 " --> pdb=" O MET C 173 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.507A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.923A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 402 through 410 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.685A pdb=" N LEU C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.546A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 483 through 507 removed outlier: 4.019A pdb=" N ARG C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 507 " --> pdb=" O ILE C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.942A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 562 Processing helix chain 'C' and resid 563 through 568 Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 606 Processing helix chain 'C' and resid 607 through 609 No H-bonds generated for 'chain 'C' and resid 607 through 609' Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 650 through 667 Processing helix chain 'C' and resid 668 through 687 removed outlier: 3.509A pdb=" N GLY C 678 " --> pdb=" O ILE C 674 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 707 Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.856A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.856A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.856A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.856A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2979 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3466 1.33 - 1.45: 5433 1.45 - 1.57: 12233 1.57 - 1.69: 56 1.69 - 1.81: 204 Bond restraints: 21392 Sorted by residual: bond pdb=" CA TYR D 213 " pdb=" C TYR D 213 " ideal model delta sigma weight residual 1.523 1.510 0.013 1.21e-02 6.83e+03 1.12e+00 bond pdb=" CA TYR A 213 " pdb=" C TYR A 213 " ideal model delta sigma weight residual 1.523 1.510 0.013 1.21e-02 6.83e+03 1.12e+00 bond pdb=" CA TYR C 213 " pdb=" C TYR C 213 " ideal model delta sigma weight residual 1.523 1.510 0.013 1.21e-02 6.83e+03 1.12e+00 bond pdb=" CA TYR B 213 " pdb=" C TYR B 213 " ideal model delta sigma weight residual 1.523 1.510 0.013 1.21e-02 6.83e+03 1.12e+00 bond pdb=" C PRO B 753 " pdb=" N GLY B 754 " ideal model delta sigma weight residual 1.330 1.315 0.016 1.49e-02 4.50e+03 1.11e+00 ... (remaining 21387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 28535 2.08 - 4.16: 173 4.16 - 6.24: 20 6.24 - 8.32: 4 8.32 - 10.40: 16 Bond angle restraints: 28748 Sorted by residual: angle pdb=" C ASP C 752 " pdb=" N PRO C 753 " pdb=" CA PRO C 753 " ideal model delta sigma weight residual 120.21 113.68 6.53 9.60e-01 1.09e+00 4.63e+01 angle pdb=" C ASP D 752 " pdb=" N PRO D 753 " pdb=" CA PRO D 753 " ideal model delta sigma weight residual 120.21 113.70 6.51 9.60e-01 1.09e+00 4.59e+01 angle pdb=" C ASP A 752 " pdb=" N PRO A 753 " pdb=" CA PRO A 753 " ideal model delta sigma weight residual 120.21 113.70 6.51 9.60e-01 1.09e+00 4.59e+01 angle pdb=" C ASP B 752 " pdb=" N PRO B 753 " pdb=" CA PRO B 753 " ideal model delta sigma weight residual 120.21 113.70 6.51 9.60e-01 1.09e+00 4.59e+01 angle pdb=" CA LEU B 711 " pdb=" CB LEU B 711 " pdb=" CG LEU B 711 " ideal model delta sigma weight residual 116.30 126.70 -10.40 3.50e+00 8.16e-02 8.83e+00 ... (remaining 28743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.33: 11532 23.33 - 46.67: 1168 46.67 - 70.00: 248 70.00 - 93.34: 48 93.34 - 116.67: 4 Dihedral angle restraints: 13000 sinusoidal: 5824 harmonic: 7176 Sorted by residual: dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual 93.00 145.39 -52.39 1 1.00e+01 1.00e-02 3.74e+01 dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual 93.00 145.39 -52.39 1 1.00e+01 1.00e-02 3.74e+01 dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual 93.00 145.38 -52.38 1 1.00e+01 1.00e-02 3.74e+01 ... (remaining 12997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1893 0.025 - 0.050: 779 0.050 - 0.075: 371 0.075 - 0.100: 73 0.100 - 0.125: 40 Chirality restraints: 3156 Sorted by residual: chirality pdb=" C2 POV B 806 " pdb=" C1 POV B 806 " pdb=" C3 POV B 806 " pdb=" O21 POV B 806 " both_signs ideal model delta sigma weight residual False 2.43 2.30 0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" C2 POV A 806 " pdb=" C1 POV A 806 " pdb=" C3 POV A 806 " pdb=" O21 POV A 806 " both_signs ideal model delta sigma weight residual False 2.43 2.30 0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL B 385 " pdb=" N VAL B 385 " pdb=" C VAL B 385 " pdb=" CB VAL B 385 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 3153 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 264 " 0.033 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO D 265 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 265 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 265 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 264 " 0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO A 265 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 264 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO C 265 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " -0.028 5.00e-02 4.00e+02 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4731 2.78 - 3.31: 18950 3.31 - 3.84: 34588 3.84 - 4.37: 40932 4.37 - 4.90: 70892 Nonbonded interactions: 170093 Sorted by model distance: nonbonded pdb=" OG SER C 328 " pdb=" OD1 ASN C 330 " model vdw 2.254 3.040 nonbonded pdb=" OG SER D 328 " pdb=" OD1 ASN D 330 " model vdw 2.254 3.040 nonbonded pdb=" OG SER A 328 " pdb=" OD1 ASN A 330 " model vdw 2.255 3.040 nonbonded pdb=" OG SER B 328 " pdb=" OD1 ASN B 330 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR B 460 " pdb=" O14 POV A 801 " model vdw 2.284 3.040 ... (remaining 170088 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' and (resid 119 through 755 or (resid 801 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P )) or resid 802 or (resid \ 803 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or n \ ame C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or \ name O31 or name O32 or name P or name C210 or name C211 or name C212)) or (res \ id 804 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or n \ ame O21 or name O22 or name O31 or name O32 or name P )) or resid 805 or (resid \ 806 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or \ name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or name \ O21 or name O22 or name O31 or name O32 or name P )) or (resid 807 and (name N \ or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C \ 2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or nam \ e C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P or name C210 or name C310 or name C311)))) selection = (chain 'B' and (resid 119 through 755 or (resid 801 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P )) or resid 802 or (resid \ 803 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or n \ ame C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or \ name O31 or name O32 or name P or name C210 or name C211 or name C212)) or (res \ id 804 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or n \ ame O21 or name O22 or name O31 or name O32 or name P )) or resid 805 or (resid \ 806 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or \ name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or name \ O21 or name O22 or name O31 or name O32 or name P )) or (resid 807 and (name N \ or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C \ 2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or nam \ e C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P or name C210 or name C310 or name C311)))) selection = (chain 'C' and (resid 119 through 801 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)) or (resid 803 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212)) or (resid 804 and (name N or name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 \ or name C23 or name C24 or name C25 or name C3 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or na \ me O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 o \ r name P )) or (resid 805 and (name N or name C1 or name C11 or name C12 or name \ C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or n \ ame C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name O11 or name O12 or name O13 or name O14 or na \ me O21 or name O22 or name O31 or name O32 or name P or name C210 or name C310 o \ r name C311)) or (resid 806 and (name N or name C1 or name C11 or name C12 or na \ me C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or \ name C24 or name C25 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or \ resid 807)) selection = (chain 'D' and (resid 119 through 801 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)) or (resid 803 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212)) or (resid 804 and (name N or name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 \ or name C23 or name C24 or name C25 or name C3 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or na \ me O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 o \ r name P )) or (resid 805 and (name N or name C1 or name C11 or name C12 or name \ C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or n \ ame C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name O11 or name O12 or name O13 or name O14 or na \ me O21 or name O22 or name O31 or name O32 or name P or name C210 or name C310 o \ r name C311)) or (resid 806 and (name N or name C1 or name C11 or name C12 or na \ me C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or \ name C24 or name C25 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or \ resid 807)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.000 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 0.026 21396 Z= 0.102 Angle : 0.514 10.400 28756 Z= 0.268 Chirality : 0.035 0.125 3156 Planarity : 0.003 0.051 3468 Dihedral : 19.021 116.671 8332 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % 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: -1.89 (0.15), residues: 2416 helix: -0.39 (0.12), residues: 1404 sheet: 0.57 (0.61), residues: 84 loop : -2.79 (0.16), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 225 TYR 0.008 0.001 TYR D 594 PHE 0.013 0.001 PHE D 728 TRP 0.011 0.001 TRP C 742 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 (21392) covalent geometry : angle 0.51406 / 0.27 (28748) SS BOND : bond 0.00088 / 0.04 ( 4) SS BOND : angle 0.28585 / 0.14 ( 8) hydrogen bonds : bond 0.16077 / 10.38 ( 1005) hydrogen bonds : angle 5.94007 / 4.14 ( 2979) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.675 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.1451 time to fit residues: 73.0058 Evaluate side-chains 292 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.0170 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.0020 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 0.6980 overall best weight: 0.4026 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.183268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.150586 restraints weight = 24673.966| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.96 r_work: 0.3446 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 21396 Z= 0.100 Angle : 0.470 8.279 28756 Z= 0.241 Chirality : 0.035 0.126 3156 Planarity : 0.004 0.048 3468 Dihedral : 13.997 108.878 3600 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.77 % Allowed : 23.70 % Favored : 74.54 % 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: -0.70 (0.16), residues: 2416 helix: 0.67 (0.13), residues: 1476 sheet: 1.36 (0.70), residues: 64 loop : -2.67 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 188 TYR 0.010 0.001 TYR D 594 PHE 0.012 0.001 PHE D 445 TRP 0.006 0.001 TRP C 692 HIS 0.005 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (21392) covalent geometry : angle 0.47000 / 0.24 (28748) SS BOND : bond 0.00082 / 0.04 ( 4) SS BOND : angle 0.17485 / 0.07 ( 8) hydrogen bonds : bond 0.03747 / 2.50 ( 1005) hydrogen bonds : angle 4.09267 / 2.87 ( 2979) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 273 time to evaluate : 0.753 Fit side-chains REVERT: D 581 LYS cc_start: 0.8239 (mmtt) cc_final: 0.8037 (mmtp) REVERT: B 581 LYS cc_start: 0.8234 (mmtt) cc_final: 0.8026 (mmtp) REVERT: C 562 MET cc_start: 0.8496 (mmm) cc_final: 0.7816 (tpp) REVERT: C 581 LYS cc_start: 0.8284 (mmtt) cc_final: 0.8084 (mmtp) outliers start: 38 outliers final: 24 residues processed: 298 average time/residue: 0.1409 time to fit residues: 67.0465 Evaluate side-chains 268 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 619 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [148, 10, 240, 206, 224, 211, 80, 141, 97, 75, 243] chunk 148 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 206 optimal weight: 0.0970 chunk 224 optimal weight: 2.9990 chunk 211 optimal weight: 0.0980 chunk 80 optimal weight: 0.7980 chunk 141 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 243 optimal weight: 0.0170 overall best weight: 0.3216 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.183478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.150001 restraints weight = 24786.326| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.02 r_work: 0.3484 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21396 Z= 0.087 Angle : 0.440 7.250 28756 Z= 0.225 Chirality : 0.035 0.124 3156 Planarity : 0.003 0.047 3468 Dihedral : 13.465 103.000 3600 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.00 % Allowed : 23.70 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2416 helix: 1.14 (0.14), residues: 1476 sheet: 1.26 (0.68), residues: 64 loop : -2.64 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 416 TYR 0.009 0.001 TYR D 594 PHE 0.009 0.001 PHE C 250 TRP 0.006 0.001 TRP A 739 HIS 0.004 0.001 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.09 (21392) covalent geometry : angle 0.44035 / 0.23 (28748) SS BOND : bond 0.00047 / 0.02 ( 4) SS BOND : angle 0.13084 / 0.06 ( 8) hydrogen bonds : bond 0.03337 / 2.22 ( 1005) hydrogen bonds : angle 3.79058 / 2.67 ( 2979) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.8305 (mmm) cc_final: 0.7631 (tpp) REVERT: D 562 MET cc_start: 0.8303 (mmm) cc_final: 0.7636 (tpp) REVERT: B 562 MET cc_start: 0.8304 (mmm) cc_final: 0.7635 (tpp) outliers start: 43 outliers final: 29 residues processed: 327 average time/residue: 0.1373 time to fit residues: 72.0276 Evaluate side-chains 294 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 619 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [72, 125, 15, 118, 236, 66, 83, 74, 192, 185, 140] chunk 72 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 118 optimal weight: 0.3980 chunk 236 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 192 optimal weight: 0.2980 chunk 185 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 647 ASN A 683 ASN A 750 ASN D 647 ASN D 683 ASN D 750 ASN B 647 ASN B 683 ASN B 750 ASN C 683 ASN C 750 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.179636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.145235 restraints weight = 24703.105| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.99 r_work: 0.3366 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 21396 Z= 0.116 Angle : 0.477 7.021 28756 Z= 0.244 Chirality : 0.036 0.126 3156 Planarity : 0.004 0.048 3468 Dihedral : 13.420 107.716 3600 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.35 % Allowed : 23.28 % Favored : 73.37 % 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: -0.20 (0.17), residues: 2416 helix: 1.17 (0.14), residues: 1468 sheet: 1.36 (0.69), residues: 64 loop : -2.62 (0.17), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 295 TYR 0.012 0.001 TYR D 451 PHE 0.009 0.001 PHE C 590 TRP 0.007 0.001 TRP C 692 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (21392) covalent geometry : angle 0.47682 / 0.24 (28748) SS BOND : bond 0.00090 / 0.04 ( 4) SS BOND : angle 0.15499 / 0.06 ( 8) hydrogen bonds : bond 0.03548 / 2.37 ( 1005) hydrogen bonds : angle 3.83573 / 2.70 ( 2979) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 272 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7430 (t70) REVERT: A 562 MET cc_start: 0.8361 (mmm) cc_final: 0.7748 (tpp) REVERT: D 426 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.7392 (t70) REVERT: D 562 MET cc_start: 0.8413 (mmm) cc_final: 0.7805 (tpp) REVERT: B 426 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.7432 (t70) REVERT: B 562 MET cc_start: 0.8362 (mmm) cc_final: 0.7754 (tpp) REVERT: C 426 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7424 (t70) outliers start: 72 outliers final: 52 residues processed: 330 average time/residue: 0.1324 time to fit residues: 71.3266 Evaluate side-chains 314 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 258 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 619 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [241, 191, 45, 172, 167, 16, 100, 203, 51, 61, 89] chunk 241 optimal weight: 0.7980 chunk 191 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 100 optimal weight: 6.9990 chunk 203 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 89 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 647 ASN C 647 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.179808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145286 restraints weight = 24552.023| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.93 r_work: 0.3405 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 21396 Z= 0.109 Angle : 0.473 7.023 28756 Z= 0.241 Chirality : 0.036 0.124 3156 Planarity : 0.003 0.049 3468 Dihedral : 13.244 107.396 3600 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.39 % Allowed : 23.14 % Favored : 73.47 % 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 (0.17), residues: 2416 helix: 1.18 (0.14), residues: 1476 sheet: 1.27 (0.67), residues: 64 loop : -2.64 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 375 TYR 0.011 0.001 TYR B 451 PHE 0.008 0.001 PHE A 538 TRP 0.007 0.001 TRP A 692 HIS 0.004 0.001 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (21392) covalent geometry : angle 0.47303 / 0.24 (28748) SS BOND : bond 0.00075 / 0.04 ( 4) SS BOND : angle 0.11925 / 0.05 ( 8) hydrogen bonds : bond 0.03433 / 2.28 ( 1005) hydrogen bonds : angle 3.76730 / 2.65 ( 2979) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 267 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.7604 (t70) REVERT: A 562 MET cc_start: 0.8574 (mmm) cc_final: 0.7971 (tpp) REVERT: A 586 ASP cc_start: 0.8494 (p0) cc_final: 0.8104 (p0) REVERT: D 426 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7612 (t70) REVERT: D 562 MET cc_start: 0.8593 (mmm) cc_final: 0.7989 (tpp) REVERT: B 426 HIS cc_start: 0.7881 (OUTLIER) cc_final: 0.7617 (t70) REVERT: B 562 MET cc_start: 0.8580 (mmm) cc_final: 0.7974 (tpp) REVERT: C 426 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7614 (t70) outliers start: 73 outliers final: 51 residues processed: 326 average time/residue: 0.1295 time to fit residues: 68.2394 Evaluate side-chains 320 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 265 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 619 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [45, 184, 76, 62, 187, 49, 109, 172, 142, 95, 165] chunk 45 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 76 optimal weight: 0.0770 chunk 62 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 49 optimal weight: 0.2980 chunk 109 optimal weight: 0.0970 chunk 172 optimal weight: 0.0000 chunk 142 optimal weight: 0.0370 chunk 95 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 overall best weight: 0.1018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 683 ASN A 735 ASN D 683 ASN D 735 ASN B 683 ASN B 735 ASN C 683 ASN C 735 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.184921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.152483 restraints weight = 24861.113| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.86 r_work: 0.3532 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21396 Z= 0.081 Angle : 0.450 9.024 28756 Z= 0.225 Chirality : 0.034 0.130 3156 Planarity : 0.003 0.048 3468 Dihedral : 12.559 95.949 3600 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.00 % Allowed : 23.75 % Favored : 74.26 % 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: 0.11 (0.17), residues: 2416 helix: 1.43 (0.14), residues: 1484 sheet: 1.30 (0.67), residues: 64 loop : -2.57 (0.17), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 416 TYR 0.007 0.001 TYR C 594 PHE 0.009 0.001 PHE A 542 TRP 0.009 0.001 TRP D 739 HIS 0.004 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00168 / 0.08 (21392) covalent geometry : angle 0.45003 / 0.22 (28748) SS BOND : bond 0.00006 / 0.00 ( 4) SS BOND : angle 0.13667 / 0.07 ( 8) hydrogen bonds : bond 0.02864 / 1.91 ( 1005) hydrogen bonds : angle 3.54001 / 2.50 ( 2979) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 311 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 GLN cc_start: 0.8077 (mt0) cc_final: 0.7764 (mt0) REVERT: A 686 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7621 (mptt) REVERT: A 717 MET cc_start: 0.5732 (mtt) cc_final: 0.5480 (mtt) REVERT: D 279 GLN cc_start: 0.8053 (mt0) cc_final: 0.7744 (mt0) REVERT: D 686 LYS cc_start: 0.8410 (mtmt) cc_final: 0.8197 (mtmm) REVERT: D 717 MET cc_start: 0.5739 (mtt) cc_final: 0.5473 (mtt) REVERT: B 279 GLN cc_start: 0.8059 (mt0) cc_final: 0.7756 (mt0) REVERT: B 686 LYS cc_start: 0.8405 (mtmt) cc_final: 0.8195 (mtmm) REVERT: B 717 MET cc_start: 0.5742 (mtt) cc_final: 0.5485 (mtt) REVERT: C 279 GLN cc_start: 0.8062 (mt0) cc_final: 0.7750 (mt0) REVERT: C 717 MET cc_start: 0.5745 (mtt) cc_final: 0.5502 (mtt) outliers start: 43 outliers final: 37 residues processed: 345 average time/residue: 0.1336 time to fit residues: 73.9676 Evaluate side-chains 329 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 292 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 619 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [116, 62, 78, 8, 3, 165, 93, 220, 126, 151, 169] chunk 116 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 220 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN A 647 ASN A 735 ASN D 178 ASN D 647 ASN D 735 ASN B 178 ASN B 735 ASN C 178 ASN C 647 ASN C 735 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.176836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143767 restraints weight = 24727.902| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.75 r_work: 0.3316 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21396 Z= 0.172 Angle : 0.545 9.317 28756 Z= 0.275 Chirality : 0.038 0.131 3156 Planarity : 0.004 0.050 3468 Dihedral : 13.247 110.310 3600 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.16 % Allowed : 23.28 % Favored : 73.56 % 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: -0.26 (0.17), residues: 2416 helix: 1.04 (0.13), residues: 1500 sheet: 0.94 (0.67), residues: 64 loop : -2.58 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 225 TYR 0.015 0.002 TYR D 451 PHE 0.010 0.001 PHE A 590 TRP 0.007 0.001 TRP A 493 HIS 0.008 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (21392) covalent geometry : angle 0.54549 / 0.28 (28748) SS BOND : bond 0.00143 / 0.07 ( 4) SS BOND : angle 0.21368 / 0.09 ( 8) hydrogen bonds : bond 0.03846 / 2.55 ( 1005) hydrogen bonds : angle 3.91806 / 2.75 ( 2979) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 270 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7414 (t70) REVERT: A 586 ASP cc_start: 0.8426 (p0) cc_final: 0.8025 (p0) REVERT: A 686 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7779 (mptt) REVERT: A 748 PHE cc_start: 0.7306 (p90) cc_final: 0.6902 (p90) REVERT: D 426 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.7409 (t70) REVERT: D 686 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8262 (mtmm) REVERT: B 426 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.7418 (t70) REVERT: C 426 HIS cc_start: 0.7717 (OUTLIER) cc_final: 0.7418 (t70) outliers start: 68 outliers final: 53 residues processed: 327 average time/residue: 0.1333 time to fit residues: 69.8866 Evaluate side-chains 328 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 271 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 619 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [202, 94, 195, 74, 219, 155, 2, 41, 26, 40, 190] chunk 202 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 195 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 219 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 190 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN D 178 ASN B 178 ASN C 178 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.179472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146803 restraints weight = 24501.879| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.72 r_work: 0.3383 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21396 Z= 0.105 Angle : 0.493 9.195 28756 Z= 0.248 Chirality : 0.036 0.128 3156 Planarity : 0.003 0.050 3468 Dihedral : 12.880 107.208 3600 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.65 % Allowed : 23.75 % Favored : 73.61 % 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: -0.15 (0.17), residues: 2416 helix: 1.13 (0.13), residues: 1500 sheet: 0.95 (0.66), residues: 64 loop : -2.54 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 188 TYR 0.010 0.001 TYR D 451 PHE 0.008 0.001 PHE A 538 TRP 0.007 0.001 TRP D 692 HIS 0.008 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (21392) covalent geometry : angle 0.49278 / 0.25 (28748) SS BOND : bond 0.00055 / 0.03 ( 4) SS BOND : angle 0.12353 / 0.06 ( 8) hydrogen bonds : bond 0.03400 / 2.26 ( 1005) hydrogen bonds : angle 3.75549 / 2.65 ( 2979) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 277 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8258 (mp) REVERT: A 586 ASP cc_start: 0.8360 (p0) cc_final: 0.7995 (p0) REVERT: A 686 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7705 (mptt) REVERT: D 443 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8258 (mp) REVERT: B 443 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8256 (mp) REVERT: C 443 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8263 (mp) REVERT: C 586 ASP cc_start: 0.8453 (p0) cc_final: 0.8078 (p0) outliers start: 57 outliers final: 46 residues processed: 325 average time/residue: 0.1285 time to fit residues: 67.8006 Evaluate side-chains 314 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 264 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 619 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [27, 210, 71, 222, 130, 213, 212, 243, 226, 182, 120] chunk 27 optimal weight: 0.5980 chunk 210 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 226 optimal weight: 0.9980 chunk 182 optimal weight: 0.3980 chunk 120 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN A 647 ASN D 178 ASN D 647 ASN B 178 ASN B 647 ASN C 178 ASN C 647 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.176867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142988 restraints weight = 24638.573| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.80 r_work: 0.3398 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21396 Z= 0.157 Angle : 0.536 9.393 28756 Z= 0.271 Chirality : 0.038 0.129 3156 Planarity : 0.004 0.050 3468 Dihedral : 13.106 113.513 3600 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.08 % Favored : 92.88 % Rotamer: Outliers : 2.93 % Allowed : 23.65 % Favored : 73.42 % 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: -0.32 (0.17), residues: 2416 helix: 1.01 (0.13), residues: 1492 sheet: 0.78 (0.66), residues: 64 loop : -2.59 (0.17), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 188 TYR 0.015 0.002 TYR C 451 PHE 0.011 0.001 PHE B 590 TRP 0.007 0.001 TRP A 692 HIS 0.008 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (21392) covalent geometry : angle 0.53595 / 0.27 (28748) SS BOND : bond 0.00123 / 0.06 ( 4) SS BOND : angle 0.15891 / 0.07 ( 8) hydrogen bonds : bond 0.03757 / 2.49 ( 1005) hydrogen bonds : angle 3.89502 / 2.73 ( 2979) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 269 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8276 (mp) REVERT: A 586 ASP cc_start: 0.8387 (p0) cc_final: 0.8004 (p0) REVERT: A 686 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7768 (mptt) REVERT: D 443 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8277 (mp) REVERT: B 443 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8271 (mp) REVERT: B 586 ASP cc_start: 0.8492 (p0) cc_final: 0.8080 (p0) REVERT: B 748 PHE cc_start: 0.7336 (p90) cc_final: 0.6864 (p90) REVERT: C 443 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8279 (mp) REVERT: C 586 ASP cc_start: 0.8490 (p0) cc_final: 0.8102 (p0) REVERT: C 748 PHE cc_start: 0.7345 (p90) cc_final: 0.6857 (p90) outliers start: 63 outliers final: 54 residues processed: 323 average time/residue: 0.1312 time to fit residues: 68.6087 Evaluate side-chains 327 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain C residue 691 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [150, 69, 139, 242, 82, 120, 239, 44, 149, 201, 77] chunk 150 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 242 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 239 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN A 647 ASN D 160 HIS D 178 ASN D 647 ASN B 178 ASN C 160 HIS C 178 ASN C 647 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.178926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144677 restraints weight = 24796.760| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.86 r_work: 0.3379 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21396 Z= 0.106 Angle : 0.497 9.168 28756 Z= 0.252 Chirality : 0.036 0.129 3156 Planarity : 0.004 0.051 3468 Dihedral : 12.807 109.761 3600 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 2.65 % Allowed : 23.88 % Favored : 73.47 % 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 (0.17), residues: 2416 helix: 1.12 (0.13), residues: 1500 sheet: 0.70 (0.66), residues: 64 loop : -2.54 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 188 TYR 0.010 0.001 TYR B 451 PHE 0.009 0.001 PHE A 542 TRP 0.008 0.001 TRP D 692 HIS 0.011 0.001 HIS D 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (21392) covalent geometry : angle 0.49706 / 0.25 (28748) SS BOND : bond 0.00059 / 0.03 ( 4) SS BOND : angle 0.13355 / 0.07 ( 8) hydrogen bonds : bond 0.03398 / 2.26 ( 1005) hydrogen bonds : angle 3.77561 / 2.66 ( 2979) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8262 (mp) REVERT: A 586 ASP cc_start: 0.8358 (p0) cc_final: 0.7975 (p0) REVERT: A 686 LYS cc_start: 0.8301 (mtmt) cc_final: 0.7735 (mptt) REVERT: D 443 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8267 (mp) REVERT: B 188 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.7200 (mtp-110) REVERT: B 419 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8323 (mtm) REVERT: B 443 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8267 (mp) REVERT: B 586 ASP cc_start: 0.8465 (p0) cc_final: 0.8076 (p0) REVERT: C 419 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8318 (mtm) REVERT: C 443 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8259 (mp) REVERT: C 586 ASP cc_start: 0.8462 (p0) cc_final: 0.8068 (p0) outliers start: 57 outliers final: 49 residues processed: 316 average time/residue: 0.1282 time to fit residues: 65.8154 Evaluate side-chains 312 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 257 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 619 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [32, 51, 103, 147, 52, 107, 115, 41, 109, 110, 78] chunk 32 optimal weight: 0.0070 chunk 51 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 115 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN A 647 ASN D 160 HIS D 178 ASN D 647 ASN B 160 HIS B 178 ASN B 647 ASN C 160 HIS C 178 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.179550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145294 restraints weight = 24660.396| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.88 r_work: 0.3417 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21396 Z= 0.101 Angle : 0.494 9.220 28756 Z= 0.250 Chirality : 0.036 0.130 3156 Planarity : 0.004 0.050 3468 Dihedral : 12.665 108.267 3600 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.33 % Favored : 93.63 % Rotamer: Outliers : 2.79 % Allowed : 23.70 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.17), residues: 2416 helix: 1.18 (0.13), residues: 1500 sheet: 0.79 (0.66), residues: 64 loop : -2.50 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 188 TYR 0.010 0.001 TYR C 451 PHE 0.010 0.001 PHE A 542 TRP 0.009 0.001 TRP A 692 HIS 0.011 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (21392) covalent geometry : angle 0.49450 / 0.25 (28748) SS BOND : bond 0.00050 / 0.03 ( 4) SS BOND : angle 0.13595 / 0.07 ( 8) hydrogen bonds : bond 0.03327 / 2.22 ( 1005) hydrogen bonds : angle 3.73196 / 2.63 ( 2979) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4951.86 seconds wall clock time: 85 minutes 33.07 seconds (5133.07 seconds total)