Starting phenix.real_space_refine on Thu Sep 18 23:02:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdm_61396/09_2025/9jdm_61396.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdm_61396/09_2025/9jdm_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_61396/09_2025/9jdm_61396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdm_61396/09_2025/9jdm_61396.map" model { file = "/net/cci-nas-00/data/ceres_data/9jdm_61396/09_2025/9jdm_61396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdm_61396/09_2025/9jdm_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-2.0-5805/lib/python3.9/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: 7.78, per 1000 atoms: 0.37 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=3, 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 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: 1.92 Conformation dependent library (CDL) restraints added in 866.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.40 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: 3.29 Time building geometry restraints manager: 2.54 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: 11531 23.33 - 46.67: 1167 46.67 - 70.00: 247 70.00 - 93.34: 48 93.34 - 116.67: 4 Dihedral angle restraints: 12997 sinusoidal: 5821 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 D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual 93.00 145.34 -52.34 1 1.00e+01 1.00e-02 3.74e+01 ... (remaining 12994 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: 2.03 - 2.61: 225 2.61 - 3.18: 16763 3.18 - 3.75: 32849 3.75 - 4.33: 44888 4.33 - 4.90: 75371 Nonbonded interactions: 170096 Sorted by model distance: nonbonded pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " model vdw 2.032 3.760 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 ... (remaining 170091 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.800 Find NCS groups from input model: 0.510 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 21395 Z= 0.102 Angle : 0.514 10.400 28754 Z= 0.268 Chirality : 0.035 0.125 3156 Planarity : 0.003 0.051 3468 Dihedral : 19.021 116.671 8332 Min Nonbonded Distance : 2.032 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 aren 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 covalent geometry : bond 0.00197 (21392) covalent geometry : angle 0.51406 (28748) SS BOND : bond 0.00086 ( 3) SS BOND : angle 0.28930 ( 6) hydrogen bonds : bond 0.16077 ( 1005) hydrogen bonds : angle 5.94007 ( 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 : 0.732 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.1520 time to fit residues: 76.1459 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 : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.183093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.149731 restraints weight = 24669.248| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.93 r_work: 0.3447 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 21395 Z= 0.098 Angle : 0.470 8.253 28754 Z= 0.242 Chirality : 0.035 0.130 3156 Planarity : 0.004 0.048 3468 Dihedral : 14.012 109.054 3600 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.95 % Allowed : 23.61 % Favored : 74.44 % 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 aren not related in a simple way. whole: -0.70 (0.16), residues: 2416 helix: 0.67 (0.13), residues: 1476 sheet: 1.35 (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 A 445 TRP 0.007 0.001 TRP C 559 HIS 0.005 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00210 (21392) covalent geometry : angle 0.47030 (28748) SS BOND : bond 0.00113 ( 3) SS BOND : angle 0.21261 ( 6) hydrogen bonds : bond 0.03736 ( 1005) hydrogen bonds : angle 4.09459 ( 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 317 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 275 time to evaluate : 0.601 Fit side-chains REVERT: A 574 MET cc_start: 0.8735 (mmm) cc_final: 0.8477 (mtt) REVERT: A 581 LYS cc_start: 0.8237 (mmtt) cc_final: 0.8032 (mmtp) REVERT: D 574 MET cc_start: 0.8743 (mmm) cc_final: 0.8474 (mtt) REVERT: D 581 LYS cc_start: 0.8235 (mmtt) cc_final: 0.8031 (mmtp) REVERT: B 574 MET cc_start: 0.8733 (mmm) cc_final: 0.8461 (mtt) REVERT: B 581 LYS cc_start: 0.8239 (mmtt) cc_final: 0.8031 (mmtp) REVERT: C 562 MET cc_start: 0.8231 (mmm) cc_final: 0.7582 (tpp) REVERT: C 574 MET cc_start: 0.8759 (mmm) cc_final: 0.8486 (mtt) REVERT: C 581 LYS cc_start: 0.8272 (mmtt) cc_final: 0.8066 (mmtp) outliers start: 42 outliers final: 29 residues processed: 303 average time/residue: 0.1366 time to fit residues: 66.3235 Evaluate side-chains 276 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 247 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 388 SER 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 284 HIS Chi-restraints excluded: chain D residue 323 MET 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 619 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 284 HIS 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 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 388 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 563 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 148 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 240 optimal weight: 0.0370 chunk 206 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN C 683 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.180314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145976 restraints weight = 24740.016| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.11 r_work: 0.3409 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 21395 Z= 0.111 Angle : 0.466 7.298 28754 Z= 0.240 Chirality : 0.036 0.123 3156 Planarity : 0.004 0.049 3468 Dihedral : 13.694 109.544 3600 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.37 % Allowed : 24.07 % 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 aren not related in a simple way. whole: -0.37 (0.17), residues: 2416 helix: 1.00 (0.13), residues: 1476 sheet: 1.31 (0.69), residues: 64 loop : -2.67 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 295 TYR 0.012 0.001 TYR D 451 PHE 0.013 0.001 PHE B 250 TRP 0.007 0.001 TRP C 692 HIS 0.005 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00253 (21392) covalent geometry : angle 0.46627 (28748) SS BOND : bond 0.00092 ( 3) SS BOND : angle 0.18130 ( 6) hydrogen bonds : bond 0.03646 ( 1005) hydrogen bonds : angle 3.92817 ( 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 322 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 271 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 562 MET cc_start: 0.8560 (mmm) cc_final: 0.7918 (tpp) outliers start: 51 outliers final: 33 residues processed: 314 average time/residue: 0.1317 time to fit residues: 66.5886 Evaluate side-chains 291 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 213 TYR 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 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 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 213 TYR 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 213 TYR 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 603 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 72 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 15 optimal weight: 0.0870 chunk 118 optimal weight: 5.9990 chunk 236 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN A 750 ASN D 647 ASN D 750 ASN B 750 ASN C 683 ASN C 750 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.179498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145709 restraints weight = 24701.830| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.86 r_work: 0.3345 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 21395 Z= 0.114 Angle : 0.474 7.226 28754 Z= 0.243 Chirality : 0.036 0.124 3156 Planarity : 0.004 0.050 3468 Dihedral : 13.412 110.174 3600 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.97 % Allowed : 23.19 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.17), residues: 2416 helix: 1.10 (0.14), residues: 1476 sheet: 1.27 (0.68), residues: 64 loop : -2.67 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 375 TYR 0.011 0.001 TYR D 451 PHE 0.011 0.001 PHE B 250 TRP 0.007 0.001 TRP C 692 HIS 0.005 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00262 (21392) covalent geometry : angle 0.47371 (28748) SS BOND : bond 0.00084 ( 3) SS BOND : angle 0.14364 ( 6) hydrogen bonds : bond 0.03527 ( 1005) hydrogen bonds : angle 3.83368 ( 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: 64 poor density : 280 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7437 (t70) REVERT: A 562 MET cc_start: 0.8381 (mmm) cc_final: 0.7793 (tpp) REVERT: D 426 HIS cc_start: 0.7689 (OUTLIER) cc_final: 0.7430 (t70) REVERT: D 562 MET cc_start: 0.8373 (mmm) cc_final: 0.7786 (tpp) REVERT: B 426 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.7446 (t70) REVERT: B 562 MET cc_start: 0.8385 (mmm) cc_final: 0.7803 (tpp) REVERT: C 426 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7430 (t70) REVERT: C 562 MET cc_start: 0.8339 (mmm) cc_final: 0.7901 (tpp) outliers start: 64 outliers final: 46 residues processed: 333 average time/residue: 0.1276 time to fit residues: 68.8463 Evaluate side-chains 316 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 266 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 177 LEU 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 426 HIS Chi-restraints excluded: chain A residue 513 LEU 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 241 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 172 optimal weight: 0.3980 chunk 167 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 203 optimal weight: 0.0470 chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 89 optimal weight: 0.4980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.179912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.146377 restraints weight = 24565.839| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.79 r_work: 0.3394 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 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 = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21395 Z= 0.104 Angle : 0.466 7.127 28754 Z= 0.237 Chirality : 0.036 0.124 3156 Planarity : 0.003 0.049 3468 Dihedral : 13.105 108.533 3600 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.74 % Allowed : 23.51 % Favored : 73.75 % 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 aren not related in a simple way. whole: -0.20 (0.17), residues: 2416 helix: 1.18 (0.14), residues: 1476 sheet: 1.27 (0.68), residues: 64 loop : -2.67 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 375 TYR 0.010 0.001 TYR D 451 PHE 0.009 0.001 PHE B 250 TRP 0.008 0.001 TRP C 692 HIS 0.005 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00238 (21392) covalent geometry : angle 0.46591 (28748) SS BOND : bond 0.00067 ( 3) SS BOND : angle 0.11749 ( 6) hydrogen bonds : bond 0.03405 ( 1005) hydrogen bonds : angle 3.76502 ( 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 342 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 283 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LEU cc_start: 0.8079 (pt) cc_final: 0.7663 (pt) REVERT: A 426 HIS cc_start: 0.7665 (OUTLIER) cc_final: 0.7411 (t70) REVERT: A 562 MET cc_start: 0.8349 (mmm) cc_final: 0.7752 (tpp) REVERT: D 370 LEU cc_start: 0.8049 (pt) cc_final: 0.7636 (pt) REVERT: D 426 HIS cc_start: 0.7668 (OUTLIER) cc_final: 0.7416 (t70) REVERT: D 562 MET cc_start: 0.8356 (mmm) cc_final: 0.7758 (tpp) REVERT: B 370 LEU cc_start: 0.8043 (pt) cc_final: 0.7630 (pt) REVERT: B 426 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.7423 (t70) REVERT: B 562 MET cc_start: 0.8348 (mmm) cc_final: 0.7752 (tpp) REVERT: C 370 LEU cc_start: 0.8084 (pt) cc_final: 0.7667 (pt) REVERT: C 426 HIS cc_start: 0.7667 (OUTLIER) cc_final: 0.7418 (t70) REVERT: C 562 MET cc_start: 0.8338 (mmm) cc_final: 0.7732 (tpp) outliers start: 59 outliers final: 40 residues processed: 334 average time/residue: 0.1328 time to fit residues: 71.6485 Evaluate side-chains 321 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 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 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 426 HIS 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 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 426 HIS 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 45 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 165 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN D 178 ASN D 647 ASN C 178 ASN C 683 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.178712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.146010 restraints weight = 24613.007| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.91 r_work: 0.3424 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21395 Z= 0.120 Angle : 0.484 6.838 28754 Z= 0.248 Chirality : 0.036 0.127 3156 Planarity : 0.004 0.050 3468 Dihedral : 13.062 110.473 3600 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.72 % Allowed : 22.40 % Favored : 73.88 % 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 aren not related in a simple way. whole: -0.25 (0.17), residues: 2416 helix: 1.04 (0.13), residues: 1500 sheet: 1.18 (0.68), residues: 64 loop : -2.58 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 225 TYR 0.012 0.001 TYR B 451 PHE 0.009 0.001 PHE B 250 TRP 0.008 0.001 TRP D 692 HIS 0.005 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00280 (21392) covalent geometry : angle 0.48393 (28748) SS BOND : bond 0.00083 ( 3) SS BOND : angle 0.12175 ( 6) hydrogen bonds : bond 0.03541 ( 1005) hydrogen bonds : angle 3.80830 ( 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 355 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 275 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.7621 (t70) REVERT: A 443 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8341 (mp) REVERT: A 562 MET cc_start: 0.8632 (mmm) cc_final: 0.8042 (tpp) REVERT: A 586 ASP cc_start: 0.8524 (p0) cc_final: 0.8145 (p0) REVERT: D 426 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.7618 (t70) REVERT: D 443 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8352 (mp) REVERT: D 562 MET cc_start: 0.8639 (mmm) cc_final: 0.8050 (tpp) REVERT: D 586 ASP cc_start: 0.8517 (p0) cc_final: 0.8111 (p0) REVERT: B 426 HIS cc_start: 0.7948 (OUTLIER) cc_final: 0.7627 (t70) REVERT: B 443 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8338 (mp) REVERT: B 562 MET cc_start: 0.8625 (mmm) cc_final: 0.8034 (tpp) REVERT: B 586 ASP cc_start: 0.8517 (p0) cc_final: 0.8118 (p0) REVERT: C 426 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7615 (t70) REVERT: C 443 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8345 (mp) REVERT: C 562 MET cc_start: 0.8613 (mmm) cc_final: 0.8014 (tpp) REVERT: C 586 ASP cc_start: 0.8529 (p0) cc_final: 0.8154 (p0) outliers start: 80 outliers final: 61 residues processed: 337 average time/residue: 0.1222 time to fit residues: 66.6555 Evaluate side-chains 336 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 267 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 177 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 426 HIS 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 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 178 ASN Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 426 HIS 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 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 418 GLU Chi-restraints excluded: chain B residue 426 HIS 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 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 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 418 GLU Chi-restraints excluded: chain C residue 426 HIS 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 537 VAL Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 603 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 116 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 169 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 647 ASN D 178 ASN B 178 ASN C 178 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.178852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.145036 restraints weight = 24650.665| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.84 r_work: 0.3367 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21395 Z= 0.111 Angle : 0.477 9.457 28754 Z= 0.243 Chirality : 0.036 0.127 3156 Planarity : 0.004 0.050 3468 Dihedral : 12.958 109.439 3600 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.58 % Allowed : 22.54 % Favored : 73.88 % 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 aren not related in a simple way. whole: -0.21 (0.17), residues: 2416 helix: 1.07 (0.13), residues: 1500 sheet: 1.17 (0.68), residues: 64 loop : -2.56 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 188 TYR 0.011 0.001 TYR D 451 PHE 0.009 0.001 PHE A 538 TRP 0.008 0.001 TRP A 692 HIS 0.005 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00256 (21392) covalent geometry : angle 0.47674 (28748) SS BOND : bond 0.00070 ( 3) SS BOND : angle 0.12680 ( 6) hydrogen bonds : bond 0.03469 ( 1005) hydrogen bonds : angle 3.77506 ( 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 361 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 284 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.7382 (t70) REVERT: A 443 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8258 (mp) REVERT: A 562 MET cc_start: 0.8391 (mmm) cc_final: 0.7800 (tpp) REVERT: A 586 ASP cc_start: 0.8455 (p0) cc_final: 0.8069 (p0) REVERT: A 686 LYS cc_start: 0.8362 (mtmt) cc_final: 0.7812 (mptt) REVERT: D 426 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7383 (t70) REVERT: D 443 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8258 (mp) REVERT: D 562 MET cc_start: 0.8405 (mmm) cc_final: 0.7812 (tpp) REVERT: D 586 ASP cc_start: 0.8437 (p0) cc_final: 0.8031 (p0) REVERT: D 686 LYS cc_start: 0.8349 (mtmt) cc_final: 0.7796 (mptt) REVERT: B 426 HIS cc_start: 0.7690 (OUTLIER) cc_final: 0.7380 (t70) REVERT: B 443 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8248 (mp) REVERT: B 562 MET cc_start: 0.8393 (mmm) cc_final: 0.7804 (tpp) REVERT: B 586 ASP cc_start: 0.8445 (p0) cc_final: 0.8067 (p0) REVERT: B 686 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7806 (mptt) REVERT: C 283 GLU cc_start: 0.7403 (pm20) cc_final: 0.7201 (pm20) REVERT: C 426 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7383 (t70) REVERT: C 443 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8261 (mp) REVERT: C 562 MET cc_start: 0.8401 (mmm) cc_final: 0.7808 (tpp) REVERT: C 586 ASP cc_start: 0.8455 (p0) cc_final: 0.8071 (p0) REVERT: C 686 LYS cc_start: 0.8350 (mtmt) cc_final: 0.7792 (mptt) outliers start: 77 outliers final: 63 residues processed: 347 average time/residue: 0.1214 time to fit residues: 66.9536 Evaluate side-chains 348 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 277 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 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 217 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 426 HIS 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 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 178 ASN Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 426 HIS 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 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 178 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 426 HIS 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 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 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 418 GLU Chi-restraints excluded: chain C residue 426 HIS 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 537 VAL Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 603 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 202 optimal weight: 0.9990 chunk 94 optimal weight: 0.0770 chunk 195 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 219 optimal weight: 0.2980 chunk 155 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 647 ASN B 178 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.179063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145236 restraints weight = 24526.625| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.87 r_work: 0.3355 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 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 = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21395 Z= 0.109 Angle : 0.482 9.395 28754 Z= 0.245 Chirality : 0.036 0.128 3156 Planarity : 0.004 0.051 3468 Dihedral : 12.893 108.779 3600 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.81 % Allowed : 22.30 % Favored : 73.88 % 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 aren not related in a simple way. whole: -0.17 (0.17), residues: 2416 helix: 1.10 (0.13), residues: 1500 sheet: 1.21 (0.68), 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 0.011 0.001 TYR C 451 PHE 0.009 0.001 PHE C 538 TRP 0.008 0.001 TRP A 692 HIS 0.005 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00250 (21392) covalent geometry : angle 0.48184 (28748) SS BOND : bond 0.00065 ( 3) SS BOND : angle 0.12776 ( 6) hydrogen bonds : bond 0.03428 ( 1005) hydrogen bonds : angle 3.75613 ( 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 364 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 282 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7374 (t70) REVERT: A 443 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8249 (mp) REVERT: A 562 MET cc_start: 0.8384 (mmm) cc_final: 0.7791 (tpp) REVERT: A 586 ASP cc_start: 0.8437 (p0) cc_final: 0.8045 (p0) REVERT: A 686 LYS cc_start: 0.8366 (mtmt) cc_final: 0.7809 (mptt) REVERT: D 426 HIS cc_start: 0.7673 (OUTLIER) cc_final: 0.7368 (t70) REVERT: D 443 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8255 (mp) REVERT: D 562 MET cc_start: 0.8390 (mmm) cc_final: 0.7794 (tpp) REVERT: D 586 ASP cc_start: 0.8423 (p0) cc_final: 0.8044 (p0) REVERT: D 686 LYS cc_start: 0.8346 (mtmt) cc_final: 0.7790 (mptt) REVERT: B 426 HIS cc_start: 0.7678 (OUTLIER) cc_final: 0.7371 (t70) REVERT: B 443 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8247 (mp) REVERT: B 562 MET cc_start: 0.8395 (mmm) cc_final: 0.7804 (tpp) REVERT: B 586 ASP cc_start: 0.8431 (p0) cc_final: 0.8040 (p0) REVERT: B 686 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7787 (mptt) REVERT: C 426 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.7377 (t70) REVERT: C 443 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8255 (mp) REVERT: C 562 MET cc_start: 0.8407 (mmm) cc_final: 0.7812 (tpp) REVERT: C 586 ASP cc_start: 0.8423 (p0) cc_final: 0.8015 (p0) REVERT: C 686 LYS cc_start: 0.8347 (mtmt) cc_final: 0.7791 (mptt) outliers start: 82 outliers final: 64 residues processed: 345 average time/residue: 0.1295 time to fit residues: 71.0223 Evaluate side-chains 350 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 278 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 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 217 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 426 HIS 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 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 178 ASN Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 426 HIS 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 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 178 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 426 HIS 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 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 178 ASN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 217 THR 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 418 GLU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 426 HIS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 27 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 chunk 212 optimal weight: 0.7980 chunk 243 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN D 178 ASN C 178 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.177696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.145425 restraints weight = 24593.328| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.06 r_work: 0.3414 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21395 Z= 0.131 Angle : 0.504 9.397 28754 Z= 0.257 Chirality : 0.037 0.129 3156 Planarity : 0.004 0.051 3468 Dihedral : 12.982 111.322 3600 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.62 % Allowed : 22.77 % 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 aren not related in a simple way. whole: -0.24 (0.17), residues: 2416 helix: 1.04 (0.13), residues: 1500 sheet: 1.11 (0.69), residues: 64 loop : -2.55 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 188 TYR 0.013 0.001 TYR C 451 PHE 0.009 0.001 PHE D 538 TRP 0.008 0.001 TRP C 692 HIS 0.005 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00310 (21392) covalent geometry : angle 0.50372 (28748) SS BOND : bond 0.00092 ( 3) SS BOND : angle 0.13652 ( 6) hydrogen bonds : bond 0.03606 ( 1005) hydrogen bonds : angle 3.81480 ( 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 361 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 283 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7597 (t70) REVERT: A 443 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8321 (mp) REVERT: A 562 MET cc_start: 0.8668 (mmm) cc_final: 0.8059 (tpp) REVERT: A 586 ASP cc_start: 0.8482 (p0) cc_final: 0.8073 (p0) REVERT: A 686 LYS cc_start: 0.8395 (mtmt) cc_final: 0.7820 (mptt) REVERT: A 748 PHE cc_start: 0.7131 (p90) cc_final: 0.6779 (p90) REVERT: D 426 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.7583 (t70) REVERT: D 443 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8325 (mp) REVERT: D 562 MET cc_start: 0.8674 (mmm) cc_final: 0.8065 (tpp) REVERT: D 586 ASP cc_start: 0.8499 (p0) cc_final: 0.8093 (p0) REVERT: D 686 LYS cc_start: 0.8391 (mtmt) cc_final: 0.7816 (mptt) REVERT: B 426 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7586 (t70) REVERT: B 443 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8320 (mp) REVERT: B 562 MET cc_start: 0.8676 (mmm) cc_final: 0.8071 (tpp) REVERT: B 586 ASP cc_start: 0.8489 (p0) cc_final: 0.8092 (p0) REVERT: B 686 LYS cc_start: 0.8388 (mtmt) cc_final: 0.7814 (mptt) REVERT: C 426 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.7589 (t70) REVERT: C 443 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8320 (mp) REVERT: C 562 MET cc_start: 0.8658 (mmm) cc_final: 0.8046 (tpp) REVERT: C 586 ASP cc_start: 0.8493 (p0) cc_final: 0.8089 (p0) REVERT: C 686 LYS cc_start: 0.8378 (mtmt) cc_final: 0.7808 (mptt) outliers start: 78 outliers final: 63 residues processed: 340 average time/residue: 0.1218 time to fit residues: 65.8471 Evaluate side-chains 351 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 280 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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 217 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 426 HIS 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 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 178 ASN Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 426 HIS 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 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 178 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 426 HIS 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 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 178 ASN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 217 THR 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 426 HIS 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 537 VAL Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 603 VAL 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: chunk 150 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 242 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 239 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN D 178 ASN D 647 ASN B 178 ASN C 160 HIS C 178 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.177285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.142904 restraints weight = 24788.077| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.89 r_work: 0.3393 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21395 Z= 0.124 Angle : 0.502 9.330 28754 Z= 0.257 Chirality : 0.037 0.129 3156 Planarity : 0.004 0.051 3468 Dihedral : 12.966 111.129 3600 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.29 % Favored : 93.54 % Rotamer: Outliers : 3.44 % Allowed : 22.77 % Favored : 73.79 % 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 aren not related in a simple way. whole: -0.25 (0.17), residues: 2416 helix: 1.03 (0.13), residues: 1500 sheet: 1.07 (0.69), residues: 64 loop : -2.55 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 188 TYR 0.012 0.001 TYR C 451 PHE 0.009 0.001 PHE A 542 TRP 0.008 0.001 TRP C 692 HIS 0.011 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00289 (21392) covalent geometry : angle 0.50220 (28748) SS BOND : bond 0.00080 ( 3) SS BOND : angle 0.13788 ( 6) hydrogen bonds : bond 0.03582 ( 1005) hydrogen bonds : angle 3.81848 ( 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 356 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 282 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7597 (t70) REVERT: A 443 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8346 (mp) REVERT: A 562 MET cc_start: 0.8616 (mmm) cc_final: 0.8036 (tpp) REVERT: A 586 ASP cc_start: 0.8474 (p0) cc_final: 0.8105 (p0) REVERT: A 686 LYS cc_start: 0.8367 (mtmt) cc_final: 0.7789 (mptt) REVERT: D 426 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7595 (t70) REVERT: D 443 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8355 (mp) REVERT: D 562 MET cc_start: 0.8617 (mmm) cc_final: 0.8036 (tpp) REVERT: D 586 ASP cc_start: 0.8475 (p0) cc_final: 0.8061 (p0) REVERT: D 686 LYS cc_start: 0.8362 (mtmt) cc_final: 0.7784 (mptt) REVERT: B 426 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7599 (t70) REVERT: B 443 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8345 (mp) REVERT: B 562 MET cc_start: 0.8615 (mmm) cc_final: 0.8034 (tpp) REVERT: B 586 ASP cc_start: 0.8467 (p0) cc_final: 0.8093 (p0) REVERT: B 686 LYS cc_start: 0.8362 (mtmt) cc_final: 0.7786 (mptt) REVERT: C 426 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7596 (t70) REVERT: C 443 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8354 (mp) REVERT: C 562 MET cc_start: 0.8631 (mmm) cc_final: 0.8049 (tpp) REVERT: C 586 ASP cc_start: 0.8476 (p0) cc_final: 0.8062 (p0) REVERT: C 686 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7783 (mptt) outliers start: 74 outliers final: 65 residues processed: 336 average time/residue: 0.1174 time to fit residues: 63.2578 Evaluate side-chains 344 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 271 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 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 217 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 426 HIS 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 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 178 ASN Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 426 HIS 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 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 178 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 426 HIS 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 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 160 HIS 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 217 THR 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 426 HIS 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 537 VAL Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 603 VAL 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: chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 147 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 178 ASN A 647 ASN D 160 HIS B 160 HIS B 178 ASN B 647 ASN C 160 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.178019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144929 restraints weight = 24607.846| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.84 r_work: 0.3415 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 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 = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21395 Z= 0.121 Angle : 0.507 9.326 28754 Z= 0.259 Chirality : 0.037 0.129 3156 Planarity : 0.004 0.051 3468 Dihedral : 12.946 110.846 3600 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.62 % Favored : 93.21 % Rotamer: Outliers : 3.76 % Allowed : 22.68 % 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 aren not related in a simple way. whole: -0.25 (0.17), residues: 2416 helix: 1.03 (0.13), residues: 1500 sheet: 1.10 (0.68), residues: 64 loop : -2.54 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 188 TYR 0.012 0.001 TYR C 451 PHE 0.010 0.001 PHE A 542 TRP 0.008 0.001 TRP C 692 HIS 0.011 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00280 (21392) covalent geometry : angle 0.50751 (28748) SS BOND : bond 0.00076 ( 3) SS BOND : angle 0.14032 ( 6) hydrogen bonds : bond 0.03537 ( 1005) hydrogen bonds : angle 3.81248 ( 2979) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4792.83 seconds wall clock time: 82 minutes 51.97 seconds (4971.97 seconds total)