Starting phenix.real_space_refine on Sun Sep 13 06:54:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5z96_6901/09_2026/5z96_6901.cif Found real_map, /net/cci-nas-00/data/ceres_data/5z96_6901/09_2026/5z96_6901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5z96_6901/09_2026/5z96_6901.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5z96_6901/09_2026/5z96_6901.cif" model { file = "/net/cci-nas-00/data/ceres_data/5z96_6901/09_2026/5z96_6901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5z96_6901/09_2026/5z96_6901.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5z96_6901/09_2026/5z96_6901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5z96_6901/09_2026/5z96_6901.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 88 5.16 5 Na 5 4.78 5 C 14085 2.51 5 N 3537 2.21 5 O 3775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21494 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5312 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'CIS': 13, 'PCIS': 1, 'PTRANS': 25, 'TRANS': 630} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 6, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "B" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5287 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'CIS': 13, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 627} Chain breaks: 6 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 6, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "C" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5287 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'CIS': 13, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 627} Chain breaks: 6 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 6, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "D" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5287 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'CIS': 13, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 627} Chain breaks: 6 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 6, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {' NA': 2, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 124 Unusual residues: {' NA': 1, 'LPP': 2, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' NA': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' NA': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.42, per 1000 atoms: 0.21 Number of scatterers: 21494 At special positions: 0 Unit cell: (137.76, 136.53, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 4 15.00 Na 5 11.00 O 3775 8.00 N 3537 7.00 C 14085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS C 549 " - pdb=" SG CYS C 554 " distance=2.03 Simple disulfide: pdb=" SG CYS D 549 " - pdb=" SG CYS D 554 " 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: 1.74 Conformation dependent library (CDL) restraints added in 705.7 milliseconds 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5122 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 4 sheets defined 70.4% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 30 through 40 Processing helix chain 'A' and resid 44 through 54 removed outlier: 3.679A pdb=" N LYS A 49 " --> pdb=" O TYR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.641A pdb=" N ILE A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 106 removed outlier: 4.090A pdb=" N HIS A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS A 106 " --> pdb=" O HIS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 117 removed outlier: 3.639A pdb=" N LEU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.568A pdb=" N GLU A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 269 removed outlier: 3.688A pdb=" N ILE A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 304 through 315 removed outlier: 3.690A pdb=" N GLN A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.535A pdb=" N ARG A 323 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 324 " --> pdb=" O TRP A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 324' Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 339 through 346 removed outlier: 3.544A pdb=" N SER A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 384 removed outlier: 3.563A pdb=" N ILE A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 372 " --> pdb=" O CYS A 368 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 423 Proline residue: A 408 - end of helix removed outlier: 3.787A pdb=" N ASP A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 removed outlier: 4.053A pdb=" N ASP A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 457 removed outlier: 3.822A pdb=" N LEU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 490 Processing helix chain 'A' and resid 491 through 499 removed outlier: 4.205A pdb=" N THR A 497 " --> pdb=" O SER A 494 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 498 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 518 removed outlier: 3.571A pdb=" N GLN A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 542 removed outlier: 5.511A pdb=" N TYR A 540 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 574 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.760A pdb=" N VAL A 583 " --> pdb=" O ASN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 Processing helix chain 'A' and resid 611 through 628 Processing helix chain 'A' and resid 634 through 645 Processing helix chain 'A' and resid 654 through 658 removed outlier: 3.662A pdb=" N ASN A 658 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 725 Processing helix chain 'A' and resid 732 through 755 removed outlier: 4.184A pdb=" N VAL A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A 741 " --> pdb=" O LYS A 737 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY A 752 " --> pdb=" O PHE A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.679A pdb=" N LYS B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.640A pdb=" N ILE B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 106 removed outlier: 4.090A pdb=" N HIS B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 106 " --> pdb=" O HIS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 117 removed outlier: 3.641A pdb=" N LEU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 215 through 232 Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.568A pdb=" N GLU B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 269 removed outlier: 3.688A pdb=" N ILE B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 304 through 315 removed outlier: 3.689A pdb=" N GLN B 308 " --> pdb=" O PRO B 304 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 removed outlier: 3.535A pdb=" N ARG B 323 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 324 " --> pdb=" O TRP B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 324' Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.544A pdb=" N SER B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 384 removed outlier: 3.563A pdb=" N ILE B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 372 " --> pdb=" O CYS B 368 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 423 Proline residue: B 408 - end of helix removed outlier: 3.788A pdb=" N ASP B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 432 removed outlier: 4.052A pdb=" N ASP B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 457 removed outlier: 3.822A pdb=" N LEU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 490 Processing helix chain 'B' and resid 491 through 499 removed outlier: 4.206A pdb=" N THR B 497 " --> pdb=" O SER B 494 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B 498 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 518 removed outlier: 3.571A pdb=" N GLN B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 542 removed outlier: 5.511A pdb=" N TYR B 540 " --> pdb=" O GLN B 536 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 574 Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.761A pdb=" N VAL B 583 " --> pdb=" O ASN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 Processing helix chain 'B' and resid 611 through 628 Processing helix chain 'B' and resid 634 through 645 Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.663A pdb=" N ASN B 658 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 725 Processing helix chain 'B' and resid 732 through 755 removed outlier: 4.184A pdb=" N VAL B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN B 741 " --> pdb=" O LYS B 737 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE B 746 " --> pdb=" O ASP B 742 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY B 752 " --> pdb=" O PHE B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 44 through 54 removed outlier: 3.679A pdb=" N LYS C 49 " --> pdb=" O TYR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.640A pdb=" N ILE C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 106 removed outlier: 4.089A pdb=" N HIS C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS C 106 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 117 removed outlier: 3.640A pdb=" N LEU C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 152 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 215 through 232 Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.568A pdb=" N GLU C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS C 253 " --> pdb=" O LYS C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 269 removed outlier: 3.687A pdb=" N ILE C 268 " --> pdb=" O GLU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 304 through 315 removed outlier: 3.689A pdb=" N GLN C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 removed outlier: 3.535A pdb=" N ARG C 323 " --> pdb=" O GLY C 320 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG C 324 " --> pdb=" O TRP C 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 320 through 324' Processing helix chain 'C' and resid 325 through 339 Processing helix chain 'C' and resid 339 through 346 removed outlier: 3.543A pdb=" N SER C 344 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 384 removed outlier: 3.564A pdb=" N ILE C 367 " --> pdb=" O PHE C 363 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C 372 " --> pdb=" O CYS C 368 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER C 384 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 423 Proline residue: C 408 - end of helix removed outlier: 3.787A pdb=" N ASP C 423 " --> pdb=" O LYS C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 removed outlier: 4.052A pdb=" N ASP C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 457 removed outlier: 3.823A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 490 Processing helix chain 'C' and resid 491 through 499 removed outlier: 4.205A pdb=" N THR C 497 " --> pdb=" O SER C 494 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA C 498 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 518 removed outlier: 3.571A pdb=" N GLN C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU C 514 " --> pdb=" O GLY C 510 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP C 515 " --> pdb=" O ARG C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 542 removed outlier: 5.511A pdb=" N TYR C 540 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 574 Processing helix chain 'C' and resid 580 through 585 removed outlier: 3.761A pdb=" N VAL C 583 " --> pdb=" O ASN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 Processing helix chain 'C' and resid 611 through 628 Processing helix chain 'C' and resid 634 through 645 Processing helix chain 'C' and resid 654 through 658 removed outlier: 3.662A pdb=" N ASN C 658 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 725 Processing helix chain 'C' and resid 732 through 755 removed outlier: 4.184A pdb=" N VAL C 736 " --> pdb=" O THR C 732 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN C 741 " --> pdb=" O LYS C 737 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE C 746 " --> pdb=" O ASP C 742 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY C 752 " --> pdb=" O PHE C 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 40 Processing helix chain 'D' and resid 44 through 54 removed outlier: 3.679A pdb=" N LYS D 49 " --> pdb=" O TYR D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.641A pdb=" N ILE D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 removed outlier: 4.090A pdb=" N HIS D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS D 106 " --> pdb=" O HIS D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 117 removed outlier: 3.640A pdb=" N LEU D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 152 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 215 through 232 Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.569A pdb=" N GLU D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 269 removed outlier: 3.688A pdb=" N ILE D 268 " --> pdb=" O GLU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 304 through 315 removed outlier: 3.690A pdb=" N GLN D 308 " --> pdb=" O PRO D 304 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 324 removed outlier: 3.535A pdb=" N ARG D 323 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG D 324 " --> pdb=" O TRP D 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 320 through 324' Processing helix chain 'D' and resid 325 through 339 Processing helix chain 'D' and resid 339 through 346 removed outlier: 3.544A pdb=" N SER D 344 " --> pdb=" O PHE D 340 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 384 removed outlier: 3.563A pdb=" N ILE D 367 " --> pdb=" O PHE D 363 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA D 371 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 372 " --> pdb=" O CYS D 368 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 423 Proline residue: D 408 - end of helix removed outlier: 3.787A pdb=" N ASP D 423 " --> pdb=" O LYS D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 432 removed outlier: 4.052A pdb=" N ASP D 432 " --> pdb=" O ASP D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 457 removed outlier: 3.822A pdb=" N LEU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 490 Processing helix chain 'D' and resid 491 through 499 removed outlier: 4.205A pdb=" N THR D 497 " --> pdb=" O SER D 494 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA D 498 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 518 removed outlier: 3.571A pdb=" N GLN D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU D 514 " --> pdb=" O GLY D 510 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP D 515 " --> pdb=" O ARG D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 542 removed outlier: 5.512A pdb=" N TYR D 540 " --> pdb=" O GLN D 536 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 574 Processing helix chain 'D' and resid 580 through 585 removed outlier: 3.761A pdb=" N VAL D 583 " --> pdb=" O ASN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 Processing helix chain 'D' and resid 611 through 628 Processing helix chain 'D' and resid 634 through 645 Processing helix chain 'D' and resid 654 through 658 removed outlier: 3.662A pdb=" N ASN D 658 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 725 Processing helix chain 'D' and resid 732 through 755 removed outlier: 4.184A pdb=" N VAL D 736 " --> pdb=" O THR D 732 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN D 741 " --> pdb=" O LYS D 737 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE D 746 " --> pdb=" O ASP D 742 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY D 752 " --> pdb=" O PHE D 748 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 removed outlier: 3.896A pdb=" N VAL B 168 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.673A pdb=" N VAL A 168 " --> pdb=" O ILE D 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AA4, first strand: chain 'C' and resid 17 through 19 removed outlier: 3.922A pdb=" N VAL D 168 " --> pdb=" O ILE C 18 " (cutoff:3.500A) 1217 hydrogen bonds defined for protein. 3567 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: 3.78 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5746 1.33 - 1.45: 4308 1.45 - 1.58: 11791 1.58 - 1.70: 4 1.70 - 1.82: 140 Bond restraints: 21989 Sorted by residual: bond pdb=" O5 LPP A 802 " pdb=" P1 LPP A 802 " ideal model delta sigma weight residual 2.278 1.603 0.675 2.00e-02 2.50e+03 1.14e+03 bond pdb=" O5 LPP B 802 " pdb=" P1 LPP B 802 " ideal model delta sigma weight residual 2.278 1.603 0.675 2.00e-02 2.50e+03 1.14e+03 bond pdb=" O5 LPP B 803 " pdb=" P1 LPP B 803 " ideal model delta sigma weight residual 2.278 1.603 0.675 2.00e-02 2.50e+03 1.14e+03 bond pdb=" O5 LPP D 802 " pdb=" P1 LPP D 802 " ideal model delta sigma weight residual 2.278 1.603 0.675 2.00e-02 2.50e+03 1.14e+03 bond pdb=" O4 LPP B 802 " pdb=" P1 LPP B 802 " ideal model delta sigma weight residual 1.764 1.508 0.256 2.00e-02 2.50e+03 1.64e+02 ... (remaining 21984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.20: 29731 8.20 - 16.40: 76 16.40 - 24.60: 4 24.60 - 32.80: 4 32.80 - 41.00: 8 Bond angle restraints: 29823 Sorted by residual: angle pdb=" O4 LPP B 802 " pdb=" P1 LPP B 802 " pdb=" O5 LPP B 802 " ideal model delta sigma weight residual 62.99 103.99 -41.00 3.00e+00 1.11e-01 1.87e+02 angle pdb=" O4 LPP B 803 " pdb=" P1 LPP B 803 " pdb=" O5 LPP B 803 " ideal model delta sigma weight residual 62.99 103.99 -41.00 3.00e+00 1.11e-01 1.87e+02 angle pdb=" O4 LPP A 802 " pdb=" P1 LPP A 802 " pdb=" O5 LPP A 802 " ideal model delta sigma weight residual 62.99 103.99 -41.00 3.00e+00 1.11e-01 1.87e+02 angle pdb=" O4 LPP D 802 " pdb=" P1 LPP D 802 " pdb=" O5 LPP D 802 " ideal model delta sigma weight residual 62.99 103.99 -41.00 3.00e+00 1.11e-01 1.87e+02 angle pdb=" C6 LPP A 802 " pdb=" O5 LPP A 802 " pdb=" P1 LPP A 802 " ideal model delta sigma weight residual 82.33 121.49 -39.16 3.00e+00 1.11e-01 1.70e+02 ... (remaining 29818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.28: 12632 24.28 - 48.57: 397 48.57 - 72.85: 62 72.85 - 97.13: 4 97.13 - 121.42: 4 Dihedral angle restraints: 13099 sinusoidal: 5248 harmonic: 7851 Sorted by residual: dihedral pdb=" CB CYS B 549 " pdb=" SG CYS B 549 " pdb=" SG CYS B 554 " pdb=" CB CYS B 554 " ideal model delta sinusoidal sigma weight residual -86.00 -165.38 79.38 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS C 549 " pdb=" SG CYS C 549 " pdb=" SG CYS C 554 " pdb=" CB CYS C 554 " ideal model delta sinusoidal sigma weight residual -86.00 -165.36 79.36 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS D 549 " pdb=" SG CYS D 549 " pdb=" SG CYS D 554 " pdb=" CB CYS D 554 " ideal model delta sinusoidal sigma weight residual -86.00 -165.35 79.35 1 1.00e+01 1.00e-02 7.83e+01 ... (remaining 13096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2883 0.080 - 0.161: 435 0.161 - 0.241: 49 0.241 - 0.321: 17 0.321 - 0.401: 13 Chirality restraints: 3397 Sorted by residual: chirality pdb=" CBG Y01 D 801 " pdb=" CAQ Y01 D 801 " pdb=" CBD Y01 D 801 " pdb=" CBI Y01 D 801 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CBF Y01 A 801 " pdb=" CAS Y01 A 801 " pdb=" CBD Y01 A 801 " pdb=" CBH Y01 A 801 " both_signs ideal model delta sigma weight residual False -2.45 -2.84 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CBG Y01 B 801 " pdb=" CAQ Y01 B 801 " pdb=" CBD Y01 B 801 " pdb=" CBI Y01 B 801 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 3394 not shown) Planarity restraints: 3689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 397 " -0.047 5.00e-02 4.00e+02 7.15e-02 8.17e+00 pdb=" N PRO B 398 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 398 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 398 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 397 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO C 398 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 398 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 398 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 397 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO D 398 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 398 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 398 " 0.040 5.00e-02 4.00e+02 ... (remaining 3686 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2905 2.75 - 3.28: 20696 3.28 - 3.82: 34365 3.82 - 4.36: 42518 4.36 - 4.90: 71454 Nonbonded interactions: 171938 Sorted by model distance: nonbonded pdb=" OH TYR C 523 " pdb=" OH TYR C 604 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR D 523 " pdb=" OH TYR D 604 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR A 523 " pdb=" OH TYR A 604 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR B 523 " pdb=" OH TYR B 604 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR D 538 " pdb=" OG1 THR D 584 " model vdw 2.262 3.040 ... (remaining 171933 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 651 or (resid 652 through 653 and (name N or na \ me CA or name C or name O or name CB )) or resid 654 through 660 or resid 692 th \ rough 801)) selection = (chain 'B' and (resid 15 through 659 or (resid 660 and (name N or name CA or nam \ e C or name O or name CB )) or resid 692 through 801)) selection = (chain 'C' and (resid 15 through 659 or (resid 660 and (name N or name CA or nam \ e C or name O or name CB )) or resid 692 through 801)) selection = (chain 'D' and (resid 15 through 659 or (resid 660 and (name N or name CA or nam \ e C or name O or name CB )) or resid 692 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.830 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.675 21993 Z= 0.641 Angle : 1.487 41.003 29831 Z= 0.730 Chirality : 0.065 0.401 3397 Planarity : 0.007 0.071 3689 Dihedral : 12.536 121.417 7965 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.75 % Favored : 93.10 % Rotamer: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.73 % Twisted Proline : 5.10 % Twisted General : 0.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.34 (0.11), residues: 2609 helix: -3.37 (0.08), residues: 1808 sheet: None (None), residues: 0 loop : -3.44 (0.17), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 716 TYR 0.023 0.004 TYR A 241 PHE 0.040 0.004 PHE C 139 TRP 0.034 0.003 TRP D 409 HIS 0.007 0.002 HIS B 369 Details of bonding type rmsd/Z covalent geometry : bond 0.01348 / 0.64 (21989) covalent geometry : angle 1.48609 / 0.73 (29823) SS BOND : bond 0.00077 / 0.04 ( 4) SS BOND : angle 3.21327 / 1.96 ( 8) hydrogen bonds : bond 0.17844 / 12.28 ( 1217) hydrogen bonds : angle 9.11049 / 6.29 ( 3567) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 666 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8218 (ttmm) REVERT: A 339 LEU cc_start: 0.9036 (mt) cc_final: 0.8728 (mp) REVERT: A 415 TRP cc_start: 0.7123 (t-100) cc_final: 0.6737 (t-100) REVERT: A 419 LYS cc_start: 0.8611 (tptm) cc_final: 0.8096 (ttmt) REVERT: A 505 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8152 (tp) REVERT: A 566 GLU cc_start: 0.7544 (tp30) cc_final: 0.7295 (tp30) REVERT: A 703 HIS cc_start: 0.7921 (t70) cc_final: 0.7622 (t70) REVERT: B 239 SER cc_start: 0.8715 (p) cc_final: 0.8511 (p) REVERT: B 339 LEU cc_start: 0.9029 (mt) cc_final: 0.8736 (mt) REVERT: B 359 ILE cc_start: 0.8851 (tt) cc_final: 0.8534 (tt) REVERT: B 404 TRP cc_start: 0.6795 (m100) cc_final: 0.5195 (t60) REVERT: B 419 LYS cc_start: 0.9025 (tptm) cc_final: 0.8734 (tptp) REVERT: B 442 ASN cc_start: 0.8775 (m-40) cc_final: 0.8468 (m110) REVERT: B 505 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8080 (tp) REVERT: B 615 MET cc_start: 0.7865 (mtt) cc_final: 0.7434 (mtt) REVERT: C 47 SER cc_start: 0.7909 (t) cc_final: 0.7655 (t) REVERT: C 95 TYR cc_start: 0.8077 (t80) cc_final: 0.7782 (t80) REVERT: C 154 ASN cc_start: 0.9132 (t0) cc_final: 0.8837 (t0) REVERT: C 232 LYS cc_start: 0.8168 (mttt) cc_final: 0.7932 (mttm) REVERT: C 239 SER cc_start: 0.9198 (p) cc_final: 0.8832 (m) REVERT: C 339 LEU cc_start: 0.8930 (mt) cc_final: 0.8541 (mt) REVERT: C 429 TYR cc_start: 0.7696 (t80) cc_final: 0.7365 (t80) REVERT: C 471 TRP cc_start: 0.8538 (m100) cc_final: 0.7975 (m-10) REVERT: C 563 THR cc_start: 0.8397 (p) cc_final: 0.7983 (t) REVERT: C 583 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8594 (t) REVERT: C 737 LYS cc_start: 0.7533 (mmtm) cc_final: 0.6969 (mmmm) REVERT: C 740 LYS cc_start: 0.8308 (tttm) cc_final: 0.8080 (mtpp) REVERT: C 751 LEU cc_start: 0.8583 (mt) cc_final: 0.8339 (mt) REVERT: D 294 LYS cc_start: 0.8334 (tttm) cc_final: 0.8133 (tmtt) REVERT: D 429 TYR cc_start: 0.7680 (t80) cc_final: 0.7456 (t80) REVERT: D 485 ASN cc_start: 0.8050 (m-40) cc_final: 0.7704 (m-40) REVERT: D 505 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8151 (tp) REVERT: D 566 GLU cc_start: 0.7422 (tp30) cc_final: 0.7097 (tp30) REVERT: D 615 MET cc_start: 0.8156 (mtt) cc_final: 0.7911 (mtt) REVERT: D 703 HIS cc_start: 0.7531 (t70) cc_final: 0.7303 (t70) outliers start: 12 outliers final: 6 residues processed: 678 average time/residue: 0.1650 time to fit residues: 168.1878 Evaluate side-chains 401 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 391 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 583 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 102 HIS ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS A 442 ASN A 535 ASN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN A 704 HIS A 741 GLN B 102 HIS B 258 GLN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS B 420 GLN B 442 ASN B 535 ASN B 559 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 ASN B 704 HIS C 80 ASN C 102 HIS C 153 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 GLN C 369 HIS C 420 GLN C 442 ASN C 535 ASN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 ASN C 703 HIS D 80 ASN D 102 HIS ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN D 369 HIS D 420 GLN D 442 ASN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 ASN D 704 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.151907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121445 restraints weight = 28048.602| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.02 r_work: 0.3080 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21993 Z= 0.163 Angle : 0.706 11.753 29831 Z= 0.363 Chirality : 0.044 0.207 3397 Planarity : 0.005 0.053 3689 Dihedral : 11.211 115.258 3098 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.06 % Favored : 94.79 % Rotamer: Outliers : 3.06 % Allowed : 10.63 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.14), residues: 2609 helix: -1.11 (0.11), residues: 1864 sheet: None (None), residues: 0 loop : -3.19 (0.18), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 296 TYR 0.020 0.002 TYR B 523 PHE 0.028 0.002 PHE A 139 TRP 0.017 0.002 TRP B 314 HIS 0.004 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (21989) covalent geometry : angle 0.70501 / 0.36 (29823) SS BOND : bond 0.01601 / 0.81 ( 4) SS BOND : angle 1.93549 / 1.20 ( 8) hydrogen bonds : bond 0.04553 / 3.12 ( 1217) hydrogen bonds : angle 4.87684 / 3.36 ( 3567) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 501 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8361 (ttmm) REVERT: A 81 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7620 (tm-30) REVERT: A 339 LEU cc_start: 0.8870 (mt) cc_final: 0.8640 (mp) REVERT: A 347 TYR cc_start: 0.8153 (t80) cc_final: 0.7952 (t80) REVERT: A 415 TRP cc_start: 0.7711 (t-100) cc_final: 0.7040 (t-100) REVERT: A 419 LYS cc_start: 0.8300 (tptm) cc_final: 0.7640 (ttmt) REVERT: A 505 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8599 (tp) REVERT: A 535 ASN cc_start: 0.9050 (t0) cc_final: 0.8794 (t0) REVERT: A 550 LYS cc_start: 0.7784 (tppp) cc_final: 0.7393 (tppp) REVERT: A 621 ASN cc_start: 0.8570 (m110) cc_final: 0.8354 (m-40) REVERT: A 703 HIS cc_start: 0.7924 (t70) cc_final: 0.7689 (t70) REVERT: A 710 MET cc_start: 0.9295 (tpp) cc_final: 0.9017 (tpp) REVERT: A 737 LYS cc_start: 0.7906 (mmtm) cc_final: 0.7467 (mmmm) REVERT: B 71 ARG cc_start: 0.7702 (mmm-85) cc_final: 0.7290 (mmp80) REVERT: B 359 ILE cc_start: 0.8855 (tt) cc_final: 0.8515 (tt) REVERT: B 404 TRP cc_start: 0.7213 (m100) cc_final: 0.5485 (t60) REVERT: B 419 LYS cc_start: 0.8559 (tptm) cc_final: 0.8219 (tptp) REVERT: B 453 ILE cc_start: 0.8222 (mm) cc_final: 0.7883 (mm) REVERT: B 505 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8425 (tp) REVERT: B 583 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9055 (t) REVERT: B 615 MET cc_start: 0.8671 (mtt) cc_final: 0.8466 (mtt) REVERT: B 619 MET cc_start: 0.8873 (ttp) cc_final: 0.8462 (ttp) REVERT: B 634 GLU cc_start: 0.7624 (tt0) cc_final: 0.7379 (mt-10) REVERT: B 737 LYS cc_start: 0.8616 (tppt) cc_final: 0.8332 (tppt) REVERT: C 47 SER cc_start: 0.8124 (t) cc_final: 0.7888 (t) REVERT: C 79 GLU cc_start: 0.8066 (tt0) cc_final: 0.7666 (tp30) REVERT: C 95 TYR cc_start: 0.8693 (t80) cc_final: 0.8247 (t80) REVERT: C 154 ASN cc_start: 0.9106 (t0) cc_final: 0.8761 (t0) REVERT: C 211 LEU cc_start: 0.8094 (mt) cc_final: 0.7879 (mt) REVERT: C 253 LYS cc_start: 0.8588 (tmtt) cc_final: 0.8300 (tptm) REVERT: C 339 LEU cc_start: 0.8830 (mt) cc_final: 0.8517 (mt) REVERT: C 470 MET cc_start: 0.7594 (tmm) cc_final: 0.7380 (tmm) REVERT: C 471 TRP cc_start: 0.8546 (m100) cc_final: 0.8188 (m100) REVERT: C 563 THR cc_start: 0.8782 (p) cc_final: 0.8410 (t) REVERT: C 619 MET cc_start: 0.9044 (ttp) cc_final: 0.8551 (ttp) REVERT: C 737 LYS cc_start: 0.7917 (mmtm) cc_final: 0.7421 (mmmm) REVERT: C 740 LYS cc_start: 0.8491 (tttm) cc_final: 0.8162 (mtpp) REVERT: D 95 TYR cc_start: 0.8230 (t80) cc_final: 0.7736 (t80) REVERT: D 154 ASN cc_start: 0.8993 (t0) cc_final: 0.8763 (t0) REVERT: D 294 LYS cc_start: 0.8786 (tttm) cc_final: 0.8345 (tmtt) REVERT: D 429 TYR cc_start: 0.8177 (t80) cc_final: 0.7898 (t80) REVERT: D 471 TRP cc_start: 0.8705 (m100) cc_final: 0.8140 (m-10) REVERT: D 550 LYS cc_start: 0.7916 (tppp) cc_final: 0.7561 (tppp) REVERT: D 619 MET cc_start: 0.8812 (mtp) cc_final: 0.8326 (ttp) REVERT: D 634 GLU cc_start: 0.7317 (tt0) cc_final: 0.7101 (mt-10) REVERT: D 710 MET cc_start: 0.9096 (tpp) cc_final: 0.8878 (tpp) REVERT: D 737 LYS cc_start: 0.7917 (mmtm) cc_final: 0.7324 (mmmt) outliers start: 68 outliers final: 33 residues processed: 545 average time/residue: 0.1559 time to fit residues: 131.1758 Evaluate side-chains 434 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 398 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 583 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 43 optimal weight: 0.5980 chunk 259 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 216 optimal weight: 2.9990 chunk 143 optimal weight: 0.1980 chunk 176 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 260 optimal weight: 0.8980 chunk 238 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 ASN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 GLN ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 472 HIS D 558 ASN D 741 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.145809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.114223 restraints weight = 28314.139| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.06 r_work: 0.3042 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21993 Z= 0.142 Angle : 0.657 11.715 29831 Z= 0.335 Chirality : 0.043 0.219 3397 Planarity : 0.004 0.048 3689 Dihedral : 10.287 117.455 3096 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.33 % Allowed : 13.19 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.16), residues: 2609 helix: 0.13 (0.12), residues: 1850 sheet: None (None), residues: 0 loop : -2.96 (0.19), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 296 TYR 0.019 0.001 TYR D 523 PHE 0.021 0.002 PHE A 139 TRP 0.015 0.001 TRP A 635 HIS 0.004 0.001 HIS B 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (21989) covalent geometry : angle 0.65565 / 0.33 (29823) SS BOND : bond 0.00403 / 0.20 ( 4) SS BOND : angle 2.55423 / 1.54 ( 8) hydrogen bonds : bond 0.04118 / 2.81 ( 1217) hydrogen bonds : angle 4.28704 / 2.97 ( 3567) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 464 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8236 (p0) cc_final: 0.7725 (p0) REVERT: A 263 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.5939 (ptm-80) REVERT: A 339 LEU cc_start: 0.8908 (mt) cc_final: 0.8690 (mp) REVERT: A 415 TRP cc_start: 0.7745 (t-100) cc_final: 0.7100 (t-100) REVERT: A 419 LYS cc_start: 0.8338 (tptm) cc_final: 0.7869 (ttmt) REVERT: A 471 TRP cc_start: 0.8615 (m100) cc_final: 0.8182 (m-10) REVERT: A 505 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8597 (tp) REVERT: A 567 THR cc_start: 0.9139 (m) cc_final: 0.8810 (m) REVERT: A 619 MET cc_start: 0.8653 (mtp) cc_final: 0.8436 (mtm) REVERT: A 737 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7467 (mmmm) REVERT: B 79 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7996 (mt-10) REVERT: B 339 LEU cc_start: 0.9045 (mp) cc_final: 0.8799 (mt) REVERT: B 359 ILE cc_start: 0.8811 (tt) cc_final: 0.8513 (tt) REVERT: B 583 VAL cc_start: 0.9375 (OUTLIER) cc_final: 0.9048 (t) REVERT: B 619 MET cc_start: 0.8988 (ttp) cc_final: 0.8699 (ttp) REVERT: B 737 LYS cc_start: 0.8672 (tppt) cc_final: 0.8381 (tppt) REVERT: C 79 GLU cc_start: 0.8155 (tt0) cc_final: 0.7707 (tp30) REVERT: C 95 TYR cc_start: 0.8805 (t80) cc_final: 0.8154 (t80) REVERT: C 154 ASN cc_start: 0.9314 (t0) cc_final: 0.9104 (t0) REVERT: C 194 ARG cc_start: 0.8460 (tpp80) cc_final: 0.8119 (tpp-160) REVERT: C 253 LYS cc_start: 0.8697 (tmtt) cc_final: 0.8398 (tptp) REVERT: C 453 ILE cc_start: 0.7958 (mm) cc_final: 0.7532 (mm) REVERT: C 471 TRP cc_start: 0.8535 (m100) cc_final: 0.7998 (m-10) REVERT: C 563 THR cc_start: 0.8843 (p) cc_final: 0.8568 (t) REVERT: C 619 MET cc_start: 0.9099 (ttp) cc_final: 0.8770 (ttp) REVERT: C 634 GLU cc_start: 0.7531 (tt0) cc_final: 0.7329 (mt-10) REVERT: C 710 MET cc_start: 0.8890 (tpp) cc_final: 0.8668 (tpp) REVERT: C 737 LYS cc_start: 0.7851 (mmtm) cc_final: 0.7438 (mmmm) REVERT: D 154 ASN cc_start: 0.9160 (t0) cc_final: 0.8944 (t0) REVERT: D 263 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.5967 (ptm-80) REVERT: D 294 LYS cc_start: 0.8861 (tttm) cc_final: 0.8454 (tmtt) REVERT: D 323 ARG cc_start: 0.6976 (tpt170) cc_final: 0.6671 (tpt170) REVERT: D 357 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8207 (mp) REVERT: D 429 TYR cc_start: 0.8065 (t80) cc_final: 0.7842 (t80) REVERT: D 710 MET cc_start: 0.9130 (tpp) cc_final: 0.8925 (tpp) REVERT: D 737 LYS cc_start: 0.8081 (mmtm) cc_final: 0.7468 (mmmm) outliers start: 74 outliers final: 41 residues processed: 511 average time/residue: 0.1539 time to fit residues: 122.2099 Evaluate side-chains 449 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 403 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 741 GLN Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 741 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 108 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 204 optimal weight: 4.9990 chunk 253 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN A 485 ASN A 506 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN B 442 ASN B 472 HIS B 506 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN C 472 HIS C 506 GLN C 585 ASN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 506 GLN ** D 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 ASN D 741 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.110053 restraints weight = 28454.778| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.03 r_work: 0.2983 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21993 Z= 0.174 Angle : 0.670 11.864 29831 Z= 0.342 Chirality : 0.044 0.222 3397 Planarity : 0.004 0.046 3689 Dihedral : 10.134 116.336 3094 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.48 % Favored : 94.37 % Rotamer: Outliers : 4.01 % Allowed : 13.60 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.16), residues: 2609 helix: 0.55 (0.12), residues: 1859 sheet: None (None), residues: 0 loop : -2.81 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 296 TYR 0.023 0.002 TYR A 523 PHE 0.019 0.002 PHE A 139 TRP 0.015 0.001 TRP D 314 HIS 0.004 0.001 HIS A 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (21989) covalent geometry : angle 0.66856 / 0.34 (29823) SS BOND : bond 0.00687 / 0.34 ( 4) SS BOND : angle 2.98932 / 1.76 ( 8) hydrogen bonds : bond 0.04214 / 2.87 ( 1217) hydrogen bonds : angle 4.19009 / 2.91 ( 3567) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 430 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8307 (p0) cc_final: 0.7676 (p0) REVERT: A 263 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.5963 (ptm-80) REVERT: A 409 TRP cc_start: 0.8623 (OUTLIER) cc_final: 0.7662 (m-90) REVERT: A 415 TRP cc_start: 0.7808 (t-100) cc_final: 0.7243 (t-100) REVERT: A 419 LYS cc_start: 0.8292 (tptm) cc_final: 0.7877 (ttmt) REVERT: A 471 TRP cc_start: 0.8568 (m100) cc_final: 0.8083 (m-10) REVERT: A 505 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8559 (tp) REVERT: A 550 LYS cc_start: 0.6873 (tppp) cc_final: 0.6554 (tppp) REVERT: A 621 ASN cc_start: 0.8692 (m110) cc_final: 0.8232 (m-40) REVERT: A 737 LYS cc_start: 0.7955 (mmtm) cc_final: 0.7524 (mmmm) REVERT: B 79 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8019 (mt-10) REVERT: B 194 ARG cc_start: 0.8537 (tpp-160) cc_final: 0.8331 (tpp80) REVERT: B 263 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6201 (ppt170) REVERT: B 359 ILE cc_start: 0.8940 (tt) cc_final: 0.8652 (tt) REVERT: B 409 TRP cc_start: 0.8594 (OUTLIER) cc_final: 0.7534 (m-90) REVERT: B 470 MET cc_start: 0.7832 (tmm) cc_final: 0.7551 (tmm) REVERT: B 583 VAL cc_start: 0.9462 (OUTLIER) cc_final: 0.9155 (t) REVERT: B 619 MET cc_start: 0.9011 (ttp) cc_final: 0.8771 (ttp) REVERT: C 71 ARG cc_start: 0.8079 (mmp80) cc_final: 0.7722 (mmm-85) REVERT: C 79 GLU cc_start: 0.8276 (tt0) cc_final: 0.7738 (mt-10) REVERT: C 95 TYR cc_start: 0.8818 (t80) cc_final: 0.8473 (t80) REVERT: C 105 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8027 (mtm-85) REVERT: C 194 ARG cc_start: 0.8457 (tpp80) cc_final: 0.8128 (tpp-160) REVERT: C 253 LYS cc_start: 0.8719 (tmtt) cc_final: 0.8495 (tptp) REVERT: C 378 PHE cc_start: 0.7922 (t80) cc_final: 0.7011 (m-10) REVERT: C 409 TRP cc_start: 0.8610 (OUTLIER) cc_final: 0.7309 (m-90) REVERT: C 453 ILE cc_start: 0.8145 (mm) cc_final: 0.7791 (mm) REVERT: C 471 TRP cc_start: 0.8569 (m100) cc_final: 0.8271 (m100) REVERT: C 556 LYS cc_start: 0.8524 (tptt) cc_final: 0.8298 (tptt) REVERT: C 563 THR cc_start: 0.8967 (p) cc_final: 0.8621 (t) REVERT: C 619 MET cc_start: 0.8976 (ttp) cc_final: 0.8727 (ttp) REVERT: C 703 HIS cc_start: 0.7524 (m90) cc_final: 0.7192 (t-90) REVERT: C 737 LYS cc_start: 0.7857 (mmtm) cc_final: 0.7444 (mmmm) REVERT: D 95 TYR cc_start: 0.8478 (t80) cc_final: 0.8157 (t80) REVERT: D 154 ASN cc_start: 0.9266 (t0) cc_final: 0.9046 (t0) REVERT: D 263 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6062 (ptm-80) REVERT: D 294 LYS cc_start: 0.8912 (tttm) cc_final: 0.8502 (tmtt) REVERT: D 324 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7674 (mtm-85) REVERT: D 359 ILE cc_start: 0.8777 (tt) cc_final: 0.8520 (tt) REVERT: D 409 TRP cc_start: 0.8588 (OUTLIER) cc_final: 0.7392 (m-90) REVERT: D 453 ILE cc_start: 0.8180 (mm) cc_final: 0.7789 (mm) REVERT: D 550 LYS cc_start: 0.7266 (tppp) cc_final: 0.7036 (tppp) REVERT: D 737 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7571 (mmmm) outliers start: 89 outliers final: 54 residues processed: 483 average time/residue: 0.1541 time to fit residues: 115.5218 Evaluate side-chains 459 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 395 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 583 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 74 optimal weight: 0.8980 chunk 141 optimal weight: 0.0040 chunk 215 optimal weight: 0.3980 chunk 120 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 157 optimal weight: 0.0980 chunk 184 optimal weight: 0.7980 chunk 155 optimal weight: 0.4980 chunk 208 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN B 80 ASN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 GLN D 247 GLN ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 585 ASN ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.145651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.114592 restraints weight = 28025.079| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.03 r_work: 0.3128 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21993 Z= 0.119 Angle : 0.608 11.539 29831 Z= 0.311 Chirality : 0.041 0.221 3397 Planarity : 0.004 0.048 3689 Dihedral : 9.623 116.547 3094 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.69 % Allowed : 15.26 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2609 helix: 0.94 (0.12), residues: 1856 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 296 TYR 0.018 0.001 TYR C 523 PHE 0.015 0.001 PHE A 340 TRP 0.014 0.001 TRP C 635 HIS 0.002 0.001 HIS A 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (21989) covalent geometry : angle 0.60703 / 0.31 (29823) SS BOND : bond 0.00853 / 0.45 ( 4) SS BOND : angle 2.12330 / 1.26 ( 8) hydrogen bonds : bond 0.03702 / 2.53 ( 1217) hydrogen bonds : angle 3.95430 / 2.74 ( 3567) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 459 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8154 (p0) cc_final: 0.7630 (p0) REVERT: A 257 ASP cc_start: 0.7759 (m-30) cc_final: 0.7551 (m-30) REVERT: A 301 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7965 (t) REVERT: A 409 TRP cc_start: 0.8578 (OUTLIER) cc_final: 0.7496 (m-90) REVERT: A 415 TRP cc_start: 0.7727 (t-100) cc_final: 0.7121 (t-100) REVERT: A 419 LYS cc_start: 0.8331 (tptm) cc_final: 0.7939 (ttmt) REVERT: A 453 ILE cc_start: 0.8086 (mm) cc_final: 0.7631 (mm) REVERT: A 567 THR cc_start: 0.9286 (m) cc_final: 0.9043 (m) REVERT: A 737 LYS cc_start: 0.7970 (mmtm) cc_final: 0.7551 (mmmm) REVERT: A 748 PHE cc_start: 0.8735 (m-80) cc_final: 0.8352 (m-10) REVERT: B 79 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7972 (mt-10) REVERT: B 87 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8126 (mm-30) REVERT: B 194 ARG cc_start: 0.8535 (tpp-160) cc_final: 0.8282 (tpp80) REVERT: B 263 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6959 (pmt-80) REVERT: B 409 TRP cc_start: 0.8468 (OUTLIER) cc_final: 0.7277 (m-90) REVERT: B 470 MET cc_start: 0.7835 (tmm) cc_final: 0.7560 (tmm) REVERT: B 583 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9107 (t) REVERT: C 95 TYR cc_start: 0.8838 (t80) cc_final: 0.8501 (t80) REVERT: C 105 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8083 (mtm-85) REVERT: C 253 LYS cc_start: 0.8621 (tmtt) cc_final: 0.8363 (tptp) REVERT: C 257 ASP cc_start: 0.7249 (m-30) cc_final: 0.6640 (m-30) REVERT: C 359 ILE cc_start: 0.8615 (tt) cc_final: 0.8383 (tt) REVERT: C 378 PHE cc_start: 0.7956 (t80) cc_final: 0.7031 (m-10) REVERT: C 409 TRP cc_start: 0.8524 (OUTLIER) cc_final: 0.7061 (m-90) REVERT: C 453 ILE cc_start: 0.8166 (mm) cc_final: 0.7808 (mm) REVERT: C 619 MET cc_start: 0.8944 (ttp) cc_final: 0.8662 (ttp) REVERT: C 703 HIS cc_start: 0.7466 (m90) cc_final: 0.7186 (t-90) REVERT: C 737 LYS cc_start: 0.7839 (mmtm) cc_final: 0.7510 (mmmm) REVERT: D 71 ARG cc_start: 0.7918 (mmm-85) cc_final: 0.7428 (mmp80) REVERT: D 95 TYR cc_start: 0.8461 (t80) cc_final: 0.8162 (t80) REVERT: D 105 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8529 (mtm180) REVERT: D 154 ASN cc_start: 0.9210 (t0) cc_final: 0.8993 (t0) REVERT: D 194 ARG cc_start: 0.8588 (tpp80) cc_final: 0.8232 (tpp-160) REVERT: D 257 ASP cc_start: 0.7710 (m-30) cc_final: 0.7508 (m-30) REVERT: D 263 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.5784 (ptm-80) REVERT: D 294 LYS cc_start: 0.8913 (tttm) cc_final: 0.8501 (tmtt) REVERT: D 324 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7616 (mtm-85) REVERT: D 357 LEU cc_start: 0.8427 (mm) cc_final: 0.8213 (mp) REVERT: D 359 ILE cc_start: 0.8593 (tt) cc_final: 0.8337 (tt) REVERT: D 409 TRP cc_start: 0.8550 (OUTLIER) cc_final: 0.7149 (m-90) REVERT: D 415 TRP cc_start: 0.8282 (t-100) cc_final: 0.7936 (t-100) REVERT: D 453 ILE cc_start: 0.8253 (mm) cc_final: 0.7860 (mm) REVERT: D 550 LYS cc_start: 0.6919 (tppp) cc_final: 0.6697 (tppp) REVERT: D 567 THR cc_start: 0.9282 (m) cc_final: 0.9049 (m) REVERT: D 737 LYS cc_start: 0.8026 (mmtm) cc_final: 0.7553 (mmmm) outliers start: 82 outliers final: 39 residues processed: 506 average time/residue: 0.1539 time to fit residues: 120.5260 Evaluate side-chains 459 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 410 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 386 HIS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 583 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 33 optimal weight: 30.0000 chunk 212 optimal weight: 0.0770 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 92 optimal weight: 0.0970 chunk 61 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 223 optimal weight: 0.1980 chunk 128 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS A 442 ASN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN B 535 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN C 308 GLN C 435 ASN C 442 ASN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 386 HIS D 442 ASN D 585 ASN ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.143193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111954 restraints weight = 28225.977| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.04 r_work: 0.3113 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21993 Z= 0.138 Angle : 0.630 12.040 29831 Z= 0.321 Chirality : 0.042 0.209 3397 Planarity : 0.004 0.048 3689 Dihedral : 9.555 116.111 3092 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.92 % Allowed : 16.48 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2609 helix: 1.12 (0.12), residues: 1844 sheet: None (None), residues: 0 loop : -2.59 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 296 TYR 0.020 0.001 TYR D 523 PHE 0.016 0.001 PHE A 340 TRP 0.013 0.001 TRP A 314 HIS 0.003 0.001 HIS B 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (21989) covalent geometry : angle 0.62928 / 0.32 (29823) SS BOND : bond 0.00311 / 0.16 ( 4) SS BOND : angle 2.02609 / 1.22 ( 8) hydrogen bonds : bond 0.03864 / 2.63 ( 1217) hydrogen bonds : angle 3.92654 / 2.72 ( 3567) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 428 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7215 (ttp-110) cc_final: 0.6747 (ttt90) REVERT: A 215 ASP cc_start: 0.8159 (p0) cc_final: 0.7642 (p0) REVERT: A 301 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.7960 (t) REVERT: A 324 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7629 (mtm-85) REVERT: A 409 TRP cc_start: 0.8590 (OUTLIER) cc_final: 0.7471 (m-90) REVERT: A 415 TRP cc_start: 0.7740 (t-100) cc_final: 0.7220 (t-100) REVERT: A 419 LYS cc_start: 0.8327 (tptm) cc_final: 0.7954 (ttmt) REVERT: A 453 ILE cc_start: 0.8251 (mm) cc_final: 0.7819 (mm) REVERT: A 532 ASN cc_start: 0.8968 (t0) cc_final: 0.8757 (t0) REVERT: A 567 THR cc_start: 0.9324 (m) cc_final: 0.9118 (m) REVERT: A 621 ASN cc_start: 0.8694 (m110) cc_final: 0.8276 (m-40) REVERT: A 737 LYS cc_start: 0.7944 (mmtm) cc_final: 0.7580 (mmmm) REVERT: A 748 PHE cc_start: 0.8779 (m-80) cc_final: 0.8446 (m-10) REVERT: B 15 ARG cc_start: 0.6889 (ttp-110) cc_final: 0.6443 (ttt90) REVERT: B 79 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8044 (mt-10) REVERT: B 194 ARG cc_start: 0.8622 (tpp-160) cc_final: 0.8333 (tpp80) REVERT: B 215 ASP cc_start: 0.8335 (p0) cc_final: 0.7656 (p0) REVERT: B 263 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6950 (pmt-80) REVERT: B 409 TRP cc_start: 0.8536 (OUTLIER) cc_final: 0.7348 (m-90) REVERT: B 583 VAL cc_start: 0.9441 (OUTLIER) cc_final: 0.9125 (t) REVERT: C 105 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8036 (mtm-85) REVERT: C 215 ASP cc_start: 0.8460 (p0) cc_final: 0.7868 (p0) REVERT: C 253 LYS cc_start: 0.8694 (tmtt) cc_final: 0.8427 (tptp) REVERT: C 257 ASP cc_start: 0.7391 (m-30) cc_final: 0.6740 (m-30) REVERT: C 359 ILE cc_start: 0.8718 (tt) cc_final: 0.8497 (tt) REVERT: C 378 PHE cc_start: 0.7963 (t80) cc_final: 0.7022 (m-10) REVERT: C 405 MET cc_start: 0.7975 (mtp) cc_final: 0.7149 (mtp) REVERT: C 409 TRP cc_start: 0.8582 (OUTLIER) cc_final: 0.7177 (m-90) REVERT: C 453 ILE cc_start: 0.8246 (mm) cc_final: 0.7893 (mm) REVERT: C 619 MET cc_start: 0.8956 (ttp) cc_final: 0.8709 (ttp) REVERT: C 703 HIS cc_start: 0.7524 (m90) cc_final: 0.7239 (t-90) REVERT: C 737 LYS cc_start: 0.7950 (mmtm) cc_final: 0.7569 (mmmm) REVERT: D 15 ARG cc_start: 0.7118 (ttp-110) cc_final: 0.6827 (ttp-110) REVERT: D 71 ARG cc_start: 0.7820 (mmm-85) cc_final: 0.7467 (mmp80) REVERT: D 105 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8455 (mtm180) REVERT: D 154 ASN cc_start: 0.9266 (t0) cc_final: 0.9050 (t0) REVERT: D 194 ARG cc_start: 0.8598 (tpp80) cc_final: 0.8261 (tpp-160) REVERT: D 294 LYS cc_start: 0.8909 (tttm) cc_final: 0.8512 (tmtt) REVERT: D 324 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7774 (mtm-85) REVERT: D 359 ILE cc_start: 0.8718 (tt) cc_final: 0.8448 (tt) REVERT: D 409 TRP cc_start: 0.8587 (OUTLIER) cc_final: 0.7207 (m-90) REVERT: D 415 TRP cc_start: 0.8292 (t-100) cc_final: 0.8013 (t-100) REVERT: D 442 ASN cc_start: 0.8919 (m-40) cc_final: 0.8675 (m110) REVERT: D 453 ILE cc_start: 0.8179 (mm) cc_final: 0.7816 (mm) REVERT: D 550 LYS cc_start: 0.6928 (tppp) cc_final: 0.6727 (tppp) REVERT: D 567 THR cc_start: 0.9334 (m) cc_final: 0.9130 (m) REVERT: D 737 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7571 (mmmm) outliers start: 87 outliers final: 57 residues processed: 480 average time/residue: 0.1406 time to fit residues: 105.1077 Evaluate side-chains 466 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 400 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 536 GLN Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 576 PHE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 HIS Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 583 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 231 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 213 optimal weight: 0.9980 chunk 263 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 203 optimal weight: 0.0010 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN B 535 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 HIS ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 ASN C 442 ASN C 585 ASN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS D 386 HIS ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.142876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111681 restraints weight = 28014.907| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.01 r_work: 0.3075 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21993 Z= 0.136 Angle : 0.633 12.277 29831 Z= 0.321 Chirality : 0.042 0.204 3397 Planarity : 0.004 0.049 3689 Dihedral : 9.489 115.888 3092 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.33 % Allowed : 17.02 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2609 helix: 1.21 (0.12), residues: 1857 sheet: None (None), residues: 0 loop : -2.48 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 296 TYR 0.021 0.001 TYR A 523 PHE 0.016 0.001 PHE D 340 TRP 0.012 0.001 TRP D 314 HIS 0.004 0.001 HIS D 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (21989) covalent geometry : angle 0.63117 / 0.32 (29823) SS BOND : bond 0.00357 / 0.18 ( 4) SS BOND : angle 2.84783 / 2.20 ( 8) hydrogen bonds : bond 0.03810 / 2.59 ( 1217) hydrogen bonds : angle 3.90845 / 2.71 ( 3567) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 421 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7049 (ttp-110) cc_final: 0.6662 (ttt90) REVERT: A 215 ASP cc_start: 0.8158 (p0) cc_final: 0.7629 (p0) REVERT: A 301 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7958 (t) REVERT: A 324 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7663 (mtm-85) REVERT: A 405 MET cc_start: 0.7730 (mtp) cc_final: 0.7040 (mtp) REVERT: A 409 TRP cc_start: 0.8606 (OUTLIER) cc_final: 0.7407 (m-90) REVERT: A 415 TRP cc_start: 0.7692 (t-100) cc_final: 0.7180 (t-100) REVERT: A 419 LYS cc_start: 0.8309 (tptm) cc_final: 0.7947 (ttmt) REVERT: A 453 ILE cc_start: 0.8269 (mm) cc_final: 0.7868 (mm) REVERT: A 489 SER cc_start: 0.9498 (t) cc_final: 0.9292 (m) REVERT: A 532 ASN cc_start: 0.8960 (t0) cc_final: 0.8746 (t0) REVERT: A 567 THR cc_start: 0.9328 (m) cc_final: 0.9127 (m) REVERT: A 621 ASN cc_start: 0.8701 (m110) cc_final: 0.8248 (m-40) REVERT: A 737 LYS cc_start: 0.8060 (mmtm) cc_final: 0.7705 (mmmm) REVERT: A 748 PHE cc_start: 0.8834 (m-80) cc_final: 0.8541 (m-10) REVERT: B 15 ARG cc_start: 0.6762 (ttp-110) cc_final: 0.6520 (ttt90) REVERT: B 79 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7967 (mt-10) REVERT: B 194 ARG cc_start: 0.8627 (tpp-160) cc_final: 0.8363 (tpp80) REVERT: B 215 ASP cc_start: 0.8344 (p0) cc_final: 0.7651 (p0) REVERT: B 263 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6888 (pmt-80) REVERT: B 409 TRP cc_start: 0.8558 (OUTLIER) cc_final: 0.7392 (m-90) REVERT: B 583 VAL cc_start: 0.9442 (OUTLIER) cc_final: 0.9141 (t) REVERT: C 15 ARG cc_start: 0.7181 (ttp-110) cc_final: 0.6684 (ttt90) REVERT: C 105 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7976 (mtm-85) REVERT: C 215 ASP cc_start: 0.8455 (p0) cc_final: 0.7923 (p0) REVERT: C 253 LYS cc_start: 0.8680 (tmtt) cc_final: 0.8381 (tptp) REVERT: C 257 ASP cc_start: 0.7424 (m-30) cc_final: 0.6726 (m-30) REVERT: C 359 ILE cc_start: 0.8716 (tt) cc_final: 0.8488 (tt) REVERT: C 378 PHE cc_start: 0.7953 (t80) cc_final: 0.7019 (m-10) REVERT: C 405 MET cc_start: 0.7921 (mtp) cc_final: 0.6969 (mtp) REVERT: C 409 TRP cc_start: 0.8573 (OUTLIER) cc_final: 0.7074 (m-90) REVERT: C 453 ILE cc_start: 0.8163 (mm) cc_final: 0.7803 (mm) REVERT: C 619 MET cc_start: 0.8994 (ttp) cc_final: 0.8763 (ttp) REVERT: C 703 HIS cc_start: 0.7474 (m90) cc_final: 0.7221 (t-90) REVERT: C 722 ILE cc_start: 0.9184 (pt) cc_final: 0.8815 (mt) REVERT: C 737 LYS cc_start: 0.8087 (mmtm) cc_final: 0.7714 (mmmm) REVERT: D 15 ARG cc_start: 0.6999 (ttp-110) cc_final: 0.6724 (ttp-110) REVERT: D 71 ARG cc_start: 0.7771 (mmm-85) cc_final: 0.7410 (mmp80) REVERT: D 105 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8444 (mtm180) REVERT: D 154 ASN cc_start: 0.9270 (t0) cc_final: 0.9060 (t0) REVERT: D 194 ARG cc_start: 0.8592 (tpp80) cc_final: 0.8254 (tpp-160) REVERT: D 294 LYS cc_start: 0.8908 (tttm) cc_final: 0.8505 (tmtt) REVERT: D 324 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7646 (mtm-85) REVERT: D 359 ILE cc_start: 0.8688 (tt) cc_final: 0.8469 (tt) REVERT: D 405 MET cc_start: 0.7763 (mtp) cc_final: 0.6987 (mtp) REVERT: D 409 TRP cc_start: 0.8610 (OUTLIER) cc_final: 0.7278 (m-90) REVERT: D 415 TRP cc_start: 0.8339 (t-100) cc_final: 0.8022 (t-100) REVERT: D 442 ASN cc_start: 0.8979 (m-40) cc_final: 0.8724 (m110) REVERT: D 453 ILE cc_start: 0.8179 (mm) cc_final: 0.7823 (mm) REVERT: D 737 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7717 (mmmt) outliers start: 74 outliers final: 53 residues processed: 463 average time/residue: 0.1472 time to fit residues: 106.7888 Evaluate side-chains 473 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 411 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 536 GLN Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain C residue 576 PHE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 HIS Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 583 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 218 optimal weight: 0.0010 chunk 208 optimal weight: 0.9980 chunk 243 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 237 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 ASN ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.144006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113125 restraints weight = 28021.973| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.00 r_work: 0.3027 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21993 Z= 0.140 Angle : 0.627 12.328 29831 Z= 0.319 Chirality : 0.042 0.209 3397 Planarity : 0.004 0.049 3689 Dihedral : 9.439 115.842 3092 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.24 % Allowed : 17.29 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.17), residues: 2609 helix: 1.25 (0.12), residues: 1867 sheet: None (None), residues: 0 loop : -2.50 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 296 TYR 0.021 0.001 TYR A 540 PHE 0.016 0.001 PHE D 340 TRP 0.012 0.001 TRP D 314 HIS 0.004 0.001 HIS B 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (21989) covalent geometry : angle 0.62575 / 0.32 (29823) SS BOND : bond 0.00219 / 0.11 ( 4) SS BOND : angle 2.65580 / 1.76 ( 8) hydrogen bonds : bond 0.03818 / 2.60 ( 1217) hydrogen bonds : angle 3.89965 / 2.71 ( 3567) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 419 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7704 (mmm-85) cc_final: 0.7219 (mmp80) REVERT: A 215 ASP cc_start: 0.8144 (p0) cc_final: 0.7592 (p0) REVERT: A 301 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7956 (t) REVERT: A 324 ARG cc_start: 0.8051 (ttm-80) cc_final: 0.7718 (mtm-85) REVERT: A 409 TRP cc_start: 0.8611 (OUTLIER) cc_final: 0.7355 (m-90) REVERT: A 415 TRP cc_start: 0.7719 (t-100) cc_final: 0.6822 (t-100) REVERT: A 419 LYS cc_start: 0.8221 (tptm) cc_final: 0.7899 (ttmt) REVERT: A 453 ILE cc_start: 0.8273 (mm) cc_final: 0.7886 (mm) REVERT: A 489 SER cc_start: 0.9509 (t) cc_final: 0.9300 (m) REVERT: A 532 ASN cc_start: 0.8958 (t0) cc_final: 0.8746 (t0) REVERT: A 621 ASN cc_start: 0.8680 (m110) cc_final: 0.8302 (m-40) REVERT: A 737 LYS cc_start: 0.8062 (mmtm) cc_final: 0.7691 (mmmt) REVERT: B 79 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7996 (mt-10) REVERT: B 194 ARG cc_start: 0.8637 (tpp-160) cc_final: 0.8370 (tpp80) REVERT: B 215 ASP cc_start: 0.8450 (p0) cc_final: 0.7773 (p0) REVERT: B 263 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6833 (pmt-80) REVERT: B 409 TRP cc_start: 0.8564 (OUTLIER) cc_final: 0.7336 (m-90) REVERT: B 583 VAL cc_start: 0.9453 (OUTLIER) cc_final: 0.9153 (t) REVERT: C 15 ARG cc_start: 0.7224 (ttp-110) cc_final: 0.6961 (ttp-110) REVERT: C 105 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7991 (mtm-85) REVERT: C 215 ASP cc_start: 0.8453 (p0) cc_final: 0.7900 (p0) REVERT: C 253 LYS cc_start: 0.8702 (tmtt) cc_final: 0.8373 (tptp) REVERT: C 257 ASP cc_start: 0.7494 (m-30) cc_final: 0.6781 (m-30) REVERT: C 359 ILE cc_start: 0.8782 (tt) cc_final: 0.8571 (tt) REVERT: C 378 PHE cc_start: 0.7933 (t80) cc_final: 0.7006 (m-10) REVERT: C 405 MET cc_start: 0.7928 (mtp) cc_final: 0.6996 (mtp) REVERT: C 409 TRP cc_start: 0.8578 (OUTLIER) cc_final: 0.7098 (m-90) REVERT: C 453 ILE cc_start: 0.8186 (mm) cc_final: 0.7833 (mm) REVERT: C 619 MET cc_start: 0.8976 (ttp) cc_final: 0.8725 (ttp) REVERT: C 703 HIS cc_start: 0.7564 (m90) cc_final: 0.7265 (t-90) REVERT: C 722 ILE cc_start: 0.9179 (pt) cc_final: 0.8888 (mt) REVERT: C 737 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7725 (mmmm) REVERT: D 15 ARG cc_start: 0.7083 (ttp-110) cc_final: 0.6450 (ttp-170) REVERT: D 71 ARG cc_start: 0.7772 (mmm-85) cc_final: 0.7419 (mmp80) REVERT: D 105 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8470 (mtm180) REVERT: D 154 ASN cc_start: 0.9275 (t0) cc_final: 0.9073 (t0) REVERT: D 194 ARG cc_start: 0.8595 (tpp80) cc_final: 0.8260 (tpp-160) REVERT: D 294 LYS cc_start: 0.8895 (tttm) cc_final: 0.8487 (tmtt) REVERT: D 324 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7592 (mtm-85) REVERT: D 359 ILE cc_start: 0.8726 (tt) cc_final: 0.8513 (tt) REVERT: D 405 MET cc_start: 0.7748 (mtp) cc_final: 0.6879 (mtp) REVERT: D 409 TRP cc_start: 0.8634 (OUTLIER) cc_final: 0.7232 (m-90) REVERT: D 415 TRP cc_start: 0.8296 (t-100) cc_final: 0.8024 (t-100) REVERT: D 442 ASN cc_start: 0.9023 (m-40) cc_final: 0.8805 (m110) REVERT: D 453 ILE cc_start: 0.8169 (mm) cc_final: 0.7820 (mm) REVERT: D 737 LYS cc_start: 0.8195 (mmtm) cc_final: 0.7816 (mmmt) outliers start: 72 outliers final: 54 residues processed: 463 average time/residue: 0.1553 time to fit residues: 111.4147 Evaluate side-chains 478 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 415 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 576 PHE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 583 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 244 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 90 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 250 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN B 535 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 HIS C 442 ASN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 386 HIS D 435 ASN ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.143138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.112067 restraints weight = 28089.418| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.01 r_work: 0.3083 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21993 Z= 0.142 Angle : 0.628 12.271 29831 Z= 0.320 Chirality : 0.042 0.220 3397 Planarity : 0.004 0.049 3689 Dihedral : 9.389 115.717 3092 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.20 % Allowed : 17.51 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2609 helix: 1.33 (0.12), residues: 1851 sheet: None (None), residues: 0 loop : -2.46 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 15 TYR 0.023 0.001 TYR A 540 PHE 0.016 0.001 PHE D 340 TRP 0.012 0.001 TRP D 314 HIS 0.004 0.001 HIS B 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (21989) covalent geometry : angle 0.62714 / 0.32 (29823) SS BOND : bond 0.00271 / 0.13 ( 4) SS BOND : angle 2.15031 / 1.34 ( 8) hydrogen bonds : bond 0.03844 / 2.61 ( 1217) hydrogen bonds : angle 3.90746 / 2.71 ( 3567) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 419 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.6716 (ttp-110) cc_final: 0.6440 (ttp-170) REVERT: A 215 ASP cc_start: 0.8128 (p0) cc_final: 0.7893 (p0) REVERT: A 294 LYS cc_start: 0.8913 (tmtt) cc_final: 0.8689 (tptt) REVERT: A 301 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7926 (t) REVERT: A 324 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7677 (mtm-85) REVERT: A 409 TRP cc_start: 0.8652 (OUTLIER) cc_final: 0.7440 (m-90) REVERT: A 415 TRP cc_start: 0.7717 (t-100) cc_final: 0.6880 (t-100) REVERT: A 419 LYS cc_start: 0.8231 (tptm) cc_final: 0.7918 (ttmt) REVERT: A 453 ILE cc_start: 0.8260 (mm) cc_final: 0.7880 (mm) REVERT: A 532 ASN cc_start: 0.8970 (t0) cc_final: 0.8759 (t0) REVERT: A 621 ASN cc_start: 0.8705 (m110) cc_final: 0.8310 (m-40) REVERT: A 737 LYS cc_start: 0.8208 (mmtm) cc_final: 0.7833 (mmmt) REVERT: B 79 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 194 ARG cc_start: 0.8610 (tpp-160) cc_final: 0.8319 (tpp80) REVERT: B 215 ASP cc_start: 0.8467 (p0) cc_final: 0.7825 (p0) REVERT: B 263 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6820 (pmt-80) REVERT: B 409 TRP cc_start: 0.8571 (OUTLIER) cc_final: 0.7250 (m-90) REVERT: B 583 VAL cc_start: 0.9481 (OUTLIER) cc_final: 0.9186 (t) REVERT: C 15 ARG cc_start: 0.7098 (ttp-110) cc_final: 0.6435 (ttp-170) REVERT: C 105 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7920 (mtm-85) REVERT: C 215 ASP cc_start: 0.8435 (p0) cc_final: 0.7860 (p0) REVERT: C 253 LYS cc_start: 0.8704 (tmtt) cc_final: 0.8365 (tptp) REVERT: C 257 ASP cc_start: 0.7510 (m-30) cc_final: 0.6749 (m-30) REVERT: C 359 ILE cc_start: 0.8814 (tt) cc_final: 0.8600 (tt) REVERT: C 378 PHE cc_start: 0.7926 (t80) cc_final: 0.7000 (m-80) REVERT: C 405 MET cc_start: 0.7934 (mtp) cc_final: 0.6967 (mtp) REVERT: C 409 TRP cc_start: 0.8630 (OUTLIER) cc_final: 0.7107 (m-90) REVERT: C 453 ILE cc_start: 0.8219 (mm) cc_final: 0.7886 (mm) REVERT: C 470 MET cc_start: 0.7760 (tmm) cc_final: 0.7494 (tmm) REVERT: C 619 MET cc_start: 0.8996 (ttp) cc_final: 0.8783 (ttp) REVERT: C 703 HIS cc_start: 0.7561 (m90) cc_final: 0.7286 (t-90) REVERT: C 722 ILE cc_start: 0.9144 (pt) cc_final: 0.8909 (mt) REVERT: C 737 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7721 (mmmm) REVERT: D 71 ARG cc_start: 0.7762 (mmm-85) cc_final: 0.7425 (mmp80) REVERT: D 105 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8445 (mtm180) REVERT: D 113 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7580 (mt-10) REVERT: D 154 ASN cc_start: 0.9294 (t0) cc_final: 0.9092 (t0) REVERT: D 194 ARG cc_start: 0.8607 (tpp80) cc_final: 0.8272 (tpp-160) REVERT: D 294 LYS cc_start: 0.8880 (tttm) cc_final: 0.8478 (tmtt) REVERT: D 324 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7585 (mtm-85) REVERT: D 359 ILE cc_start: 0.8810 (tt) cc_final: 0.8606 (tt) REVERT: D 409 TRP cc_start: 0.8676 (OUTLIER) cc_final: 0.7326 (m-90) REVERT: D 415 TRP cc_start: 0.8313 (t-100) cc_final: 0.8015 (t-100) REVERT: D 419 LYS cc_start: 0.8255 (mtpp) cc_final: 0.7764 (ttmt) REVERT: D 442 ASN cc_start: 0.9018 (m-40) cc_final: 0.8811 (m110) REVERT: D 453 ILE cc_start: 0.8242 (mm) cc_final: 0.7920 (mm) REVERT: D 556 LYS cc_start: 0.8279 (tptp) cc_final: 0.8013 (tptt) REVERT: D 737 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7842 (mmmt) outliers start: 71 outliers final: 53 residues processed: 462 average time/residue: 0.1497 time to fit residues: 107.7739 Evaluate side-chains 471 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 409 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 442 ASN Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 576 PHE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 HIS Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 583 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 186 optimal weight: 0.6980 chunk 222 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 202 optimal weight: 0.6980 chunk 116 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 203 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 HIS ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** C 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.110141 restraints weight = 28139.530| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.05 r_work: 0.3106 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21993 Z= 0.136 Angle : 0.622 12.138 29831 Z= 0.317 Chirality : 0.042 0.209 3397 Planarity : 0.004 0.049 3689 Dihedral : 9.332 115.703 3092 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.97 % Allowed : 17.51 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2609 helix: 1.37 (0.12), residues: 1851 sheet: None (None), residues: 0 loop : -2.40 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 15 TYR 0.023 0.001 TYR A 540 PHE 0.016 0.001 PHE D 340 TRP 0.012 0.001 TRP D 314 HIS 0.004 0.001 HIS B 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (21989) covalent geometry : angle 0.62108 / 0.32 (29823) SS BOND : bond 0.00266 / 0.13 ( 4) SS BOND : angle 2.24532 / 1.36 ( 8) hydrogen bonds : bond 0.03808 / 2.59 ( 1217) hydrogen bonds : angle 3.91103 / 2.72 ( 3567) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 412 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.6709 (ttp-110) cc_final: 0.6489 (ttt-90) REVERT: A 215 ASP cc_start: 0.8116 (p0) cc_final: 0.7865 (p0) REVERT: A 294 LYS cc_start: 0.8933 (tmtt) cc_final: 0.8713 (tptt) REVERT: A 301 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7925 (t) REVERT: A 324 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7682 (mtm-85) REVERT: A 409 TRP cc_start: 0.8679 (OUTLIER) cc_final: 0.7370 (m-90) REVERT: A 415 TRP cc_start: 0.7707 (t-100) cc_final: 0.6858 (t-100) REVERT: A 419 LYS cc_start: 0.8247 (tptm) cc_final: 0.7938 (ttmt) REVERT: A 453 ILE cc_start: 0.8272 (mm) cc_final: 0.7888 (mm) REVERT: A 532 ASN cc_start: 0.8986 (t0) cc_final: 0.8780 (t0) REVERT: A 621 ASN cc_start: 0.8689 (m110) cc_final: 0.8297 (m-40) REVERT: A 737 LYS cc_start: 0.8268 (mmtm) cc_final: 0.7921 (mmmt) REVERT: B 79 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8035 (mt-10) REVERT: B 194 ARG cc_start: 0.8632 (tpp-160) cc_final: 0.8353 (tpp80) REVERT: B 215 ASP cc_start: 0.8465 (p0) cc_final: 0.7839 (p0) REVERT: B 409 TRP cc_start: 0.8568 (OUTLIER) cc_final: 0.7273 (m-90) REVERT: B 583 VAL cc_start: 0.9471 (OUTLIER) cc_final: 0.9171 (t) REVERT: C 15 ARG cc_start: 0.7009 (ttp-110) cc_final: 0.6396 (ttp-170) REVERT: C 105 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.7934 (mtm-85) REVERT: C 215 ASP cc_start: 0.8395 (p0) cc_final: 0.7841 (p0) REVERT: C 324 ARG cc_start: 0.7963 (ttm-80) cc_final: 0.7737 (mtm-85) REVERT: C 359 ILE cc_start: 0.8856 (tt) cc_final: 0.8655 (tt) REVERT: C 378 PHE cc_start: 0.8000 (t80) cc_final: 0.7129 (m-80) REVERT: C 405 MET cc_start: 0.7974 (mtp) cc_final: 0.6975 (mtp) REVERT: C 409 TRP cc_start: 0.8605 (OUTLIER) cc_final: 0.7056 (m-90) REVERT: C 419 LYS cc_start: 0.8222 (mtpp) cc_final: 0.7626 (mtmt) REVERT: C 453 ILE cc_start: 0.8233 (mm) cc_final: 0.7892 (mm) REVERT: C 470 MET cc_start: 0.7772 (tmm) cc_final: 0.7499 (tmm) REVERT: C 703 HIS cc_start: 0.7581 (m90) cc_final: 0.7312 (t-90) REVERT: C 737 LYS cc_start: 0.8203 (mmtm) cc_final: 0.7773 (mmmm) REVERT: D 15 ARG cc_start: 0.7146 (ttp-110) cc_final: 0.6769 (ttt-90) REVERT: D 71 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7469 (mmp80) REVERT: D 105 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8448 (mtm180) REVERT: D 113 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7580 (mt-10) REVERT: D 194 ARG cc_start: 0.8639 (tpp80) cc_final: 0.8313 (tpp-160) REVERT: D 294 LYS cc_start: 0.8883 (tttm) cc_final: 0.8491 (tmtt) REVERT: D 324 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7644 (mtm-85) REVERT: D 409 TRP cc_start: 0.8681 (OUTLIER) cc_final: 0.7349 (m-90) REVERT: D 415 TRP cc_start: 0.8343 (t-100) cc_final: 0.8015 (t-100) REVERT: D 419 LYS cc_start: 0.8273 (mtpp) cc_final: 0.7801 (ttmt) REVERT: D 453 ILE cc_start: 0.8255 (mm) cc_final: 0.7926 (mm) REVERT: D 556 LYS cc_start: 0.8272 (tptp) cc_final: 0.8052 (tptt) REVERT: D 737 LYS cc_start: 0.8278 (mmtm) cc_final: 0.7890 (mmmt) outliers start: 66 outliers final: 51 residues processed: 457 average time/residue: 0.1593 time to fit residues: 112.7614 Evaluate side-chains 466 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 407 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 576 PHE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 583 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 206 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 221 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 212 optimal weight: 0.0020 chunk 180 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 224 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN B 535 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 386 HIS D 442 ASN D 585 ASN ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.147194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116864 restraints weight = 27852.850| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.99 r_work: 0.3120 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21993 Z= 0.130 Angle : 0.616 12.067 29831 Z= 0.314 Chirality : 0.042 0.210 3397 Planarity : 0.004 0.049 3689 Dihedral : 9.210 115.869 3092 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.15 % Allowed : 17.69 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.17), residues: 2609 helix: 1.43 (0.12), residues: 1851 sheet: None (None), residues: 0 loop : -2.37 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 15 TYR 0.025 0.001 TYR A 540 PHE 0.015 0.001 PHE D 340 TRP 0.012 0.001 TRP D 635 HIS 0.009 0.001 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (21989) covalent geometry : angle 0.61560 / 0.31 (29823) SS BOND : bond 0.00310 / 0.15 ( 4) SS BOND : angle 2.04393 / 1.23 ( 8) hydrogen bonds : bond 0.03757 / 2.55 ( 1217) hydrogen bonds : angle 3.90137 / 2.71 ( 3567) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5548.74 seconds wall clock time: 95 minutes 48.58 seconds (5748.58 seconds total)