Starting phenix.real_space_refine on Wed Sep 17 15:52:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e0h_8948/09_2025/6e0h_8948_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e0h_8948/09_2025/6e0h_8948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6e0h_8948/09_2025/6e0h_8948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e0h_8948/09_2025/6e0h_8948.map" model { file = "/net/cci-nas-00/data/ceres_data/6e0h_8948/09_2025/6e0h_8948_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e0h_8948/09_2025/6e0h_8948_neut.cif" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 38 5.16 5 C 6268 2.51 5 N 1572 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9524 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4760 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 27, 'TRANS': 558} Chain breaks: 8 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 4, 'HIS:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: A Time building chain proxies: 3.52, per 1000 atoms: 0.37 Number of scatterers: 9524 At special positions: 0 Unit cell: (126.051, 75.6309, 99.7451, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 38 16.00 O 1642 8.00 N 1572 7.00 C 6268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 345.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 2 sheets defined 70.0% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 27 through 46 removed outlier: 3.763A pdb=" N GLU B 31 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 86 removed outlier: 3.838A pdb=" N ARG B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 117 removed outlier: 3.844A pdb=" N ILE B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 117 " --> pdb=" O HIS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 removed outlier: 3.664A pdb=" N MET B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TRP B 155 " --> pdb=" O CYS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.705A pdb=" N TYR B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.556A pdb=" N PHE B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 238 removed outlier: 3.547A pdb=" N VAL B 214 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 224 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.878A pdb=" N MET B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 311 removed outlier: 3.985A pdb=" N ALA B 287 " --> pdb=" O GLN B 283 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 305 " --> pdb=" O CYS B 301 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 348 removed outlier: 3.906A pdb=" N PHE B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE B 323 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Proline residue: B 324 - end of helix removed outlier: 3.741A pdb=" N ILE B 332 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 3.809A pdb=" N THR B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 384 removed outlier: 4.055A pdb=" N LYS B 359 " --> pdb=" O GLN B 355 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 374 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Proline residue: B 377 - end of helix removed outlier: 4.053A pdb=" N THR B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.606A pdb=" N ILE B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 460 removed outlier: 3.569A pdb=" N ILE B 439 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix removed outlier: 3.641A pdb=" N PHE B 456 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 removed outlier: 3.605A pdb=" N ARG B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 525 removed outlier: 3.691A pdb=" N ASP B 511 " --> pdb=" O ASP B 507 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU B 514 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 520 " --> pdb=" O CYS B 516 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU B 522 " --> pdb=" O GLN B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 553 removed outlier: 3.585A pdb=" N SER B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 542 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 591 removed outlier: 3.580A pdb=" N GLY B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 575 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 589 " --> pdb=" O SER B 585 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 635 removed outlier: 3.844A pdb=" N SER B 617 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE B 623 " --> pdb=" O HIS B 619 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 630 " --> pdb=" O TYR B 626 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 633 " --> pdb=" O ARG B 629 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 635 " --> pdb=" O ALA B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 659 removed outlier: 3.729A pdb=" N ARG B 653 " --> pdb=" O MET B 649 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR B 654 " --> pdb=" O MET B 650 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 658 " --> pdb=" O TYR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 720 Processing helix chain 'B' and resid 721 through 724 removed outlier: 3.991A pdb=" N THR B 724 " --> pdb=" O SER B 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 721 through 724' Processing helix chain 'A' and resid 27 through 46 removed outlier: 3.762A pdb=" N GLU A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 86 removed outlier: 3.839A pdb=" N ARG A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 removed outlier: 3.845A pdb=" N ILE A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.664A pdb=" N MET A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 175 through 189 removed outlier: 3.705A pdb=" N TYR A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.556A pdb=" N PHE A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 238 removed outlier: 3.546A pdb=" N VAL A 214 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.877A pdb=" N MET A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 311 removed outlier: 3.985A pdb=" N ALA A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 305 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 348 removed outlier: 3.905A pdb=" N PHE A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 3.740A pdb=" N ILE A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.809A pdb=" N THR A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 384 removed outlier: 4.056A pdb=" N LYS A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 374 " --> pdb=" O ASN A 370 " (cutoff:3.500A) Proline residue: A 377 - end of helix removed outlier: 4.053A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 435 removed outlier: 3.606A pdb=" N ILE A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 460 removed outlier: 3.569A pdb=" N ILE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix removed outlier: 3.641A pdb=" N PHE A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS A 460 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.605A pdb=" N ARG A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 525 removed outlier: 3.691A pdb=" N ASP A 511 " --> pdb=" O ASP A 507 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 520 " --> pdb=" O CYS A 516 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 521 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 553 removed outlier: 3.585A pdb=" N SER A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 591 removed outlier: 3.579A pdb=" N GLY A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 575 " --> pdb=" O ASP A 571 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 635 removed outlier: 3.844A pdb=" N SER A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 623 " --> pdb=" O HIS A 619 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 630 " --> pdb=" O TYR A 626 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 659 removed outlier: 3.730A pdb=" N ARG A 653 " --> pdb=" O MET A 649 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 654 " --> pdb=" O MET A 650 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 658 " --> pdb=" O TYR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 720 Processing helix chain 'A' and resid 721 through 724 removed outlier: 3.991A pdb=" N THR A 724 " --> pdb=" O SER A 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 721 through 724' Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 21 removed outlier: 8.099A pdb=" N TYR B 18 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG B 65 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 20 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE B 63 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL B 62 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 52 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL B 64 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR B 50 " --> pdb=" O VAL B 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 8.099A pdb=" N TYR A 18 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG A 65 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE A 20 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 63 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL A 62 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 52 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL A 64 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR A 50 " --> pdb=" O VAL A 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 472 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2896 1.34 - 1.46: 2123 1.46 - 1.57: 4695 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 9770 Sorted by residual: bond pdb=" CB TYR A 352 " pdb=" CG TYR A 352 " ideal model delta sigma weight residual 1.512 1.455 0.057 2.20e-02 2.07e+03 6.62e+00 bond pdb=" CB TYR B 352 " pdb=" CG TYR B 352 " ideal model delta sigma weight residual 1.512 1.455 0.057 2.20e-02 2.07e+03 6.62e+00 bond pdb=" N ALA B 609 " pdb=" CA ALA B 609 " ideal model delta sigma weight residual 1.454 1.485 -0.030 1.31e-02 5.83e+03 5.38e+00 bond pdb=" N ALA A 609 " pdb=" CA ALA A 609 " ideal model delta sigma weight residual 1.454 1.485 -0.030 1.31e-02 5.83e+03 5.34e+00 bond pdb=" CB TRP A 84 " pdb=" CG TRP A 84 " ideal model delta sigma weight residual 1.498 1.428 0.070 3.10e-02 1.04e+03 5.15e+00 ... (remaining 9765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 12409 2.08 - 4.15: 693 4.15 - 6.23: 118 6.23 - 8.30: 44 8.30 - 10.38: 12 Bond angle restraints: 13276 Sorted by residual: angle pdb=" N SER A 390 " pdb=" CA SER A 390 " pdb=" C SER A 390 " ideal model delta sigma weight residual 111.28 100.90 10.38 1.09e+00 8.42e-01 9.07e+01 angle pdb=" N SER B 390 " pdb=" CA SER B 390 " pdb=" C SER B 390 " ideal model delta sigma weight residual 111.28 100.94 10.34 1.09e+00 8.42e-01 8.99e+01 angle pdb=" CA ALA A 609 " pdb=" C ALA A 609 " pdb=" N LEU A 610 " ideal model delta sigma weight residual 118.81 124.60 -5.79 1.15e+00 7.56e-01 2.54e+01 angle pdb=" CA ALA B 609 " pdb=" C ALA B 609 " pdb=" N LEU B 610 " ideal model delta sigma weight residual 118.81 124.60 -5.79 1.15e+00 7.56e-01 2.53e+01 angle pdb=" CA TYR B 352 " pdb=" CB TYR B 352 " pdb=" CG TYR B 352 " ideal model delta sigma weight residual 113.90 105.78 8.12 1.80e+00 3.09e-01 2.03e+01 ... (remaining 13271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.97: 5204 13.97 - 27.94: 404 27.94 - 41.91: 114 41.91 - 55.88: 16 55.88 - 69.85: 2 Dihedral angle restraints: 5740 sinusoidal: 2266 harmonic: 3474 Sorted by residual: dihedral pdb=" CA TRP A 155 " pdb=" C TRP A 155 " pdb=" N SER A 156 " pdb=" CA SER A 156 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA TRP B 155 " pdb=" C TRP B 155 " pdb=" N SER B 156 " pdb=" CA SER B 156 " ideal model delta harmonic sigma weight residual 180.00 155.59 24.41 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA LYS B 249 " pdb=" C LYS B 249 " pdb=" N ARG B 250 " pdb=" CA ARG B 250 " ideal model delta harmonic sigma weight residual -180.00 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 5737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 871 0.047 - 0.094: 458 0.094 - 0.141: 138 0.141 - 0.188: 25 0.188 - 0.235: 12 Chirality restraints: 1504 Sorted by residual: chirality pdb=" CA THR B 29 " pdb=" N THR B 29 " pdb=" C THR B 29 " pdb=" CB THR B 29 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA THR A 29 " pdb=" N THR A 29 " pdb=" C THR A 29 " pdb=" CB THR A 29 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA SER A 390 " pdb=" N SER A 390 " pdb=" C SER A 390 " pdb=" CB SER A 390 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1501 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 352 " 0.040 2.00e-02 2.50e+03 2.14e-02 9.14e+00 pdb=" CG TYR A 352 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 352 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 352 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR A 352 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 352 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 352 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR A 352 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 352 " 0.040 2.00e-02 2.50e+03 2.13e-02 9.09e+00 pdb=" CG TYR B 352 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 352 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 352 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 352 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 352 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 352 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR B 352 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 376 " 0.045 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 377 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.038 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2596 2.79 - 3.32: 9281 3.32 - 3.84: 15371 3.84 - 4.37: 17589 4.37 - 4.90: 28764 Nonbonded interactions: 73601 Sorted by model distance: nonbonded pdb=" OH TYR A 212 " pdb=" OG SER A 526 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR B 212 " pdb=" OG SER B 526 " model vdw 2.262 3.040 nonbonded pdb=" O VAL A 338 " pdb=" OG1 THR A 341 " model vdw 2.317 3.040 nonbonded pdb=" O ILE A 582 " pdb=" OG SER A 585 " model vdw 2.317 3.040 nonbonded pdb=" O ILE B 582 " pdb=" OG SER B 585 " model vdw 2.317 3.040 ... (remaining 73596 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.009 0.078 9770 Z= 0.397 Angle : 1.156 10.379 13276 Z= 0.640 Chirality : 0.062 0.235 1504 Planarity : 0.008 0.066 1640 Dihedral : 11.245 69.847 3472 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.40 % Allowed : 5.15 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.82 (0.17), residues: 1136 helix: -3.72 (0.11), residues: 754 sheet: -3.31 (1.18), residues: 22 loop : -3.72 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 651 TYR 0.040 0.004 TYR A 352 PHE 0.031 0.003 PHE A 388 TRP 0.033 0.004 TRP A 155 HIS 0.007 0.002 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00882 ( 9770) covalent geometry : angle 1.15557 (13276) hydrogen bonds : bond 0.30678 ( 472) hydrogen bonds : angle 10.38653 ( 1416) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 228 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 THR cc_start: 0.8582 (m) cc_final: 0.8259 (p) REVERT: B 578 TRP cc_start: 0.8629 (t-100) cc_final: 0.8325 (t60) REVERT: A 151 CYS cc_start: 0.7743 (m) cc_final: 0.7424 (m) REVERT: A 282 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8957 (tt) REVERT: A 298 ILE cc_start: 0.9318 (mt) cc_final: 0.9081 (mm) REVERT: A 499 ASN cc_start: 0.7962 (m110) cc_final: 0.6990 (m-40) outliers start: 4 outliers final: 0 residues processed: 232 average time/residue: 0.1133 time to fit residues: 34.6945 Evaluate side-chains 105 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 370 ASN B 499 ASN A 185 GLN A 370 ASN A 499 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.065277 restraints weight = 36740.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.066795 restraints weight = 21666.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.067852 restraints weight = 14951.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.068590 restraints weight = 11433.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069055 restraints weight = 9433.161| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9770 Z= 0.177 Angle : 0.759 10.521 13276 Z= 0.393 Chirality : 0.044 0.225 1504 Planarity : 0.006 0.046 1640 Dihedral : 5.944 28.067 1284 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.30 % Allowed : 3.66 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.66 (0.21), residues: 1136 helix: -1.83 (0.15), residues: 778 sheet: -2.70 (1.08), residues: 22 loop : -3.55 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 74 TYR 0.044 0.002 TYR B 352 PHE 0.018 0.002 PHE B 549 TRP 0.031 0.002 TRP B 578 HIS 0.002 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9770) covalent geometry : angle 0.75902 (13276) hydrogen bonds : bond 0.06065 ( 472) hydrogen bonds : angle 4.78915 ( 1416) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 173 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 CYS cc_start: 0.7527 (m) cc_final: 0.7230 (m) REVERT: B 191 LEU cc_start: 0.9309 (tp) cc_final: 0.9011 (tp) REVERT: B 297 ILE cc_start: 0.9260 (mm) cc_final: 0.8802 (mm) REVERT: B 529 TRP cc_start: 0.8454 (t-100) cc_final: 0.8092 (t-100) REVERT: B 570 LEU cc_start: 0.9495 (tp) cc_final: 0.9217 (tt) REVERT: A 151 CYS cc_start: 0.7515 (m) cc_final: 0.7172 (m) REVERT: A 173 PHE cc_start: 0.8734 (m-80) cc_final: 0.8221 (m-80) REVERT: A 191 LEU cc_start: 0.9277 (tp) cc_final: 0.8983 (tp) REVERT: A 297 ILE cc_start: 0.9206 (mm) cc_final: 0.8789 (mm) REVERT: A 298 ILE cc_start: 0.9601 (mt) cc_final: 0.9356 (pt) REVERT: A 352 TYR cc_start: 0.6277 (OUTLIER) cc_final: 0.6010 (m-80) REVERT: A 354 THR cc_start: 0.7867 (p) cc_final: 0.7026 (p) REVERT: A 502 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7941 (mt-10) REVERT: A 506 TYR cc_start: 0.8291 (t80) cc_final: 0.8052 (t80) outliers start: 3 outliers final: 0 residues processed: 174 average time/residue: 0.0793 time to fit residues: 20.1064 Evaluate side-chains 107 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 89 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.076204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.065835 restraints weight = 36722.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.067364 restraints weight = 21122.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068429 restraints weight = 14387.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.069150 restraints weight = 10932.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.069664 restraints weight = 9003.067| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9770 Z= 0.143 Angle : 0.681 7.534 13276 Z= 0.348 Chirality : 0.043 0.151 1504 Planarity : 0.005 0.036 1640 Dihedral : 5.417 25.573 1284 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.23), residues: 1136 helix: -0.88 (0.17), residues: 780 sheet: -1.94 (1.10), residues: 22 loop : -3.23 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 498 TYR 0.021 0.002 TYR B 352 PHE 0.012 0.001 PHE A 367 TRP 0.020 0.002 TRP B 578 HIS 0.002 0.000 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9770) covalent geometry : angle 0.68110 (13276) hydrogen bonds : bond 0.04840 ( 472) hydrogen bonds : angle 4.26885 ( 1416) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 CYS cc_start: 0.7465 (m) cc_final: 0.7212 (m) REVERT: B 173 PHE cc_start: 0.8774 (m-80) cc_final: 0.8531 (m-80) REVERT: B 191 LEU cc_start: 0.9336 (tp) cc_final: 0.8981 (tp) REVERT: B 310 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7593 (mm-30) REVERT: B 499 ASN cc_start: 0.7692 (m-40) cc_final: 0.7003 (m-40) REVERT: B 502 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7535 (mt-10) REVERT: B 529 TRP cc_start: 0.8421 (t-100) cc_final: 0.7840 (t-100) REVERT: B 564 ASP cc_start: 0.7871 (t70) cc_final: 0.7467 (t0) REVERT: B 570 LEU cc_start: 0.9458 (tp) cc_final: 0.9156 (tt) REVERT: A 151 CYS cc_start: 0.7597 (m) cc_final: 0.7174 (m) REVERT: A 173 PHE cc_start: 0.8703 (m-80) cc_final: 0.8135 (m-80) REVERT: A 191 LEU cc_start: 0.9332 (tp) cc_final: 0.9000 (tp) REVERT: A 297 ILE cc_start: 0.9007 (mm) cc_final: 0.8798 (mm) REVERT: A 499 ASN cc_start: 0.7553 (m-40) cc_final: 0.6518 (m-40) REVERT: A 502 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8039 (mt-10) REVERT: A 506 TYR cc_start: 0.8292 (t80) cc_final: 0.8058 (t80) REVERT: A 529 TRP cc_start: 0.8407 (t-100) cc_final: 0.8124 (t-100) REVERT: A 564 ASP cc_start: 0.7996 (t70) cc_final: 0.7739 (t0) REVERT: A 570 LEU cc_start: 0.9523 (tp) cc_final: 0.9244 (tt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0821 time to fit residues: 17.3440 Evaluate side-chains 106 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 0.0770 chunk 67 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.076089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.065879 restraints weight = 37440.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.067480 restraints weight = 21318.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068503 restraints weight = 14315.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069280 restraints weight = 10899.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069739 restraints weight = 8867.361| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9770 Z= 0.155 Angle : 0.683 7.457 13276 Z= 0.343 Chirality : 0.043 0.145 1504 Planarity : 0.004 0.035 1640 Dihedral : 5.121 24.546 1284 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.24), residues: 1136 helix: -0.36 (0.18), residues: 776 sheet: -1.74 (1.10), residues: 22 loop : -3.05 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.020 0.002 TYR B 352 PHE 0.013 0.001 PHE A 190 TRP 0.019 0.002 TRP B 578 HIS 0.003 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9770) covalent geometry : angle 0.68277 (13276) hydrogen bonds : bond 0.04419 ( 472) hydrogen bonds : angle 4.07666 ( 1416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 CYS cc_start: 0.7360 (m) cc_final: 0.7047 (m) REVERT: B 173 PHE cc_start: 0.8746 (m-80) cc_final: 0.8514 (m-80) REVERT: B 184 LEU cc_start: 0.9622 (mt) cc_final: 0.9318 (mt) REVERT: B 310 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 354 THR cc_start: 0.7915 (t) cc_final: 0.7578 (m) REVERT: B 499 ASN cc_start: 0.8140 (m-40) cc_final: 0.7865 (m-40) REVERT: B 529 TRP cc_start: 0.8253 (t-100) cc_final: 0.7684 (t-100) REVERT: B 564 ASP cc_start: 0.7929 (t70) cc_final: 0.7473 (t0) REVERT: A 151 CYS cc_start: 0.7537 (m) cc_final: 0.7217 (m) REVERT: A 173 PHE cc_start: 0.8660 (m-80) cc_final: 0.8132 (m-80) REVERT: A 297 ILE cc_start: 0.9046 (mm) cc_final: 0.8814 (mm) REVERT: A 499 ASN cc_start: 0.7512 (m-40) cc_final: 0.6657 (m-40) REVERT: A 529 TRP cc_start: 0.8298 (t-100) cc_final: 0.7635 (t-100) REVERT: A 570 LEU cc_start: 0.9501 (tp) cc_final: 0.9239 (tt) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0832 time to fit residues: 15.5117 Evaluate side-chains 93 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.077467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.067090 restraints weight = 36829.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.068690 restraints weight = 20939.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.069772 restraints weight = 14120.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070446 restraints weight = 10690.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.070999 restraints weight = 8867.717| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9770 Z= 0.129 Angle : 0.676 7.755 13276 Z= 0.331 Chirality : 0.043 0.166 1504 Planarity : 0.004 0.035 1640 Dihedral : 4.891 23.177 1284 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.24), residues: 1136 helix: 0.05 (0.18), residues: 772 sheet: -1.28 (1.26), residues: 18 loop : -2.95 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 74 TYR 0.020 0.001 TYR B 352 PHE 0.012 0.001 PHE B 367 TRP 0.014 0.001 TRP A 578 HIS 0.002 0.000 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9770) covalent geometry : angle 0.67619 (13276) hydrogen bonds : bond 0.04089 ( 472) hydrogen bonds : angle 3.92254 ( 1416) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 CYS cc_start: 0.7391 (m) cc_final: 0.7078 (m) REVERT: B 173 PHE cc_start: 0.8790 (m-80) cc_final: 0.8531 (m-80) REVERT: B 499 ASN cc_start: 0.7982 (m-40) cc_final: 0.7347 (m-40) REVERT: B 502 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7549 (mt-10) REVERT: B 529 TRP cc_start: 0.8158 (t-100) cc_final: 0.7351 (t-100) REVERT: A 151 CYS cc_start: 0.7501 (m) cc_final: 0.7173 (m) REVERT: A 173 PHE cc_start: 0.8727 (m-80) cc_final: 0.8194 (m-80) REVERT: A 191 LEU cc_start: 0.9357 (tp) cc_final: 0.9141 (tp) REVERT: A 225 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8162 (mm-30) REVERT: A 297 ILE cc_start: 0.9039 (mm) cc_final: 0.8797 (mm) REVERT: A 499 ASN cc_start: 0.7568 (m-40) cc_final: 0.6664 (m110) REVERT: A 529 TRP cc_start: 0.8176 (t-100) cc_final: 0.7419 (t-100) REVERT: A 570 LEU cc_start: 0.9453 (tp) cc_final: 0.9207 (tt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.0742 time to fit residues: 15.8390 Evaluate side-chains 105 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 110 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 0.0000 chunk 100 optimal weight: 1.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.078281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.068019 restraints weight = 36898.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.069624 restraints weight = 20932.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.070724 restraints weight = 14092.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.071409 restraints weight = 10622.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.071975 restraints weight = 8774.122| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9770 Z= 0.124 Angle : 0.686 7.976 13276 Z= 0.333 Chirality : 0.043 0.188 1504 Planarity : 0.004 0.035 1640 Dihedral : 4.727 21.782 1284 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.24), residues: 1136 helix: 0.22 (0.19), residues: 772 sheet: -1.05 (1.28), residues: 18 loop : -2.96 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.022 0.001 TYR B 352 PHE 0.013 0.001 PHE A 179 TRP 0.020 0.001 TRP B 578 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9770) covalent geometry : angle 0.68605 (13276) hydrogen bonds : bond 0.03975 ( 472) hydrogen bonds : angle 3.97140 ( 1416) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 150 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8403 (tp-100) REVERT: B 151 CYS cc_start: 0.7596 (m) cc_final: 0.7285 (m) REVERT: B 173 PHE cc_start: 0.8774 (m-80) cc_final: 0.8431 (m-80) REVERT: B 529 TRP cc_start: 0.8072 (t-100) cc_final: 0.7484 (t-100) REVERT: A 40 LEU cc_start: 0.8987 (mt) cc_final: 0.8775 (mt) REVERT: A 151 CYS cc_start: 0.7648 (m) cc_final: 0.7345 (m) REVERT: A 173 PHE cc_start: 0.8624 (m-80) cc_final: 0.8354 (m-80) REVERT: A 191 LEU cc_start: 0.9284 (tp) cc_final: 0.9078 (tp) REVERT: A 225 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8135 (mm-30) REVERT: A 297 ILE cc_start: 0.9037 (mm) cc_final: 0.8784 (mm) REVERT: A 529 TRP cc_start: 0.8072 (t-100) cc_final: 0.7331 (t-100) REVERT: A 570 LEU cc_start: 0.9432 (tp) cc_final: 0.9173 (tt) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.0766 time to fit residues: 16.8174 Evaluate side-chains 93 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 93 optimal weight: 0.0050 chunk 71 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN A 540 ASN A 709 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.074955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.064727 restraints weight = 37444.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.066278 restraints weight = 21669.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067360 restraints weight = 14764.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.068034 restraints weight = 11192.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068577 restraints weight = 9277.176| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9770 Z= 0.210 Angle : 0.748 7.841 13276 Z= 0.371 Chirality : 0.046 0.192 1504 Planarity : 0.004 0.033 1640 Dihedral : 4.931 23.343 1284 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.25), residues: 1136 helix: 0.23 (0.19), residues: 776 sheet: -2.00 (1.04), residues: 22 loop : -2.88 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 74 TYR 0.024 0.002 TYR B 352 PHE 0.014 0.002 PHE B 549 TRP 0.030 0.002 TRP B 578 HIS 0.005 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9770) covalent geometry : angle 0.74820 (13276) hydrogen bonds : bond 0.04288 ( 472) hydrogen bonds : angle 4.13560 ( 1416) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 CYS cc_start: 0.7833 (m) cc_final: 0.7486 (m) REVERT: B 184 LEU cc_start: 0.9610 (mt) cc_final: 0.9299 (mt) REVERT: B 529 TRP cc_start: 0.8179 (t-100) cc_final: 0.7519 (t-100) REVERT: B 590 MET cc_start: 0.8658 (ptp) cc_final: 0.8215 (ptp) REVERT: A 151 CYS cc_start: 0.8067 (m) cc_final: 0.7590 (m) REVERT: A 173 PHE cc_start: 0.8740 (m-80) cc_final: 0.8229 (m-80) REVERT: A 191 LEU cc_start: 0.9374 (tp) cc_final: 0.9098 (tp) REVERT: A 297 ILE cc_start: 0.9057 (mm) cc_final: 0.8823 (mm) REVERT: A 525 PHE cc_start: 0.9030 (m-80) cc_final: 0.8732 (m-80) REVERT: A 529 TRP cc_start: 0.8301 (t-100) cc_final: 0.7536 (t-100) REVERT: A 570 LEU cc_start: 0.9469 (tp) cc_final: 0.9252 (tt) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.0815 time to fit residues: 15.6401 Evaluate side-chains 94 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN B 540 ASN A 113 HIS A 518 GLN A 540 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.077450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.067026 restraints weight = 36953.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068586 restraints weight = 21314.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.069649 restraints weight = 14511.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070404 restraints weight = 11079.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.070822 restraints weight = 9065.151| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9770 Z= 0.130 Angle : 0.702 9.431 13276 Z= 0.342 Chirality : 0.043 0.137 1504 Planarity : 0.004 0.035 1640 Dihedral : 4.774 23.134 1284 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.25), residues: 1136 helix: 0.43 (0.19), residues: 774 sheet: -1.55 (1.17), residues: 18 loop : -2.85 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 276 TYR 0.030 0.001 TYR B 352 PHE 0.014 0.001 PHE B 549 TRP 0.024 0.002 TRP B 578 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9770) covalent geometry : angle 0.70241 (13276) hydrogen bonds : bond 0.04009 ( 472) hydrogen bonds : angle 3.99031 ( 1416) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 150 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8408 (tp-100) REVERT: B 151 CYS cc_start: 0.7937 (m) cc_final: 0.7475 (m) REVERT: B 173 PHE cc_start: 0.8797 (m-80) cc_final: 0.8449 (m-80) REVERT: B 354 THR cc_start: 0.8060 (t) cc_final: 0.7833 (m) REVERT: B 529 TRP cc_start: 0.8099 (t-100) cc_final: 0.7271 (t-100) REVERT: A 151 CYS cc_start: 0.7909 (m) cc_final: 0.7491 (m) REVERT: A 173 PHE cc_start: 0.8661 (m-80) cc_final: 0.8445 (m-80) REVERT: A 225 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8149 (mm-30) REVERT: A 297 ILE cc_start: 0.9041 (mm) cc_final: 0.8809 (mm) REVERT: A 352 TYR cc_start: 0.2688 (t80) cc_final: 0.2271 (t80) REVERT: A 529 TRP cc_start: 0.8163 (t-100) cc_final: 0.7423 (t-100) REVERT: A 570 LEU cc_start: 0.9402 (tp) cc_final: 0.9170 (tt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0764 time to fit residues: 15.8298 Evaluate side-chains 93 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 ASN B 639 ASN ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.076010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.065805 restraints weight = 37122.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.067337 restraints weight = 21342.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068349 restraints weight = 14489.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.069106 restraints weight = 11078.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.069517 restraints weight = 9088.119| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9770 Z= 0.173 Angle : 0.737 8.883 13276 Z= 0.360 Chirality : 0.045 0.168 1504 Planarity : 0.004 0.033 1640 Dihedral : 4.826 22.337 1284 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.25), residues: 1136 helix: 0.36 (0.19), residues: 786 sheet: -1.77 (1.14), residues: 18 loop : -2.68 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.031 0.002 TYR B 352 PHE 0.012 0.002 PHE B 367 TRP 0.030 0.002 TRP B 133 HIS 0.003 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9770) covalent geometry : angle 0.73671 (13276) hydrogen bonds : bond 0.04094 ( 472) hydrogen bonds : angle 4.12424 ( 1416) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 CYS cc_start: 0.7913 (m) cc_final: 0.7484 (m) REVERT: B 173 PHE cc_start: 0.8818 (m-80) cc_final: 0.8574 (m-80) REVERT: B 180 TYR cc_start: 0.8902 (t80) cc_final: 0.8609 (t80) REVERT: B 529 TRP cc_start: 0.8214 (t-100) cc_final: 0.7526 (t-100) REVERT: A 151 CYS cc_start: 0.8051 (m) cc_final: 0.7549 (m) REVERT: A 173 PHE cc_start: 0.8728 (m-80) cc_final: 0.8237 (m-80) REVERT: A 297 ILE cc_start: 0.9064 (mm) cc_final: 0.8823 (mm) REVERT: A 352 TYR cc_start: 0.2689 (t80) cc_final: 0.2393 (t80) REVERT: A 529 TRP cc_start: 0.8249 (t-100) cc_final: 0.7472 (t-100) REVERT: A 570 LEU cc_start: 0.9444 (tp) cc_final: 0.9216 (tt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.0762 time to fit residues: 14.8968 Evaluate side-chains 86 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 50 optimal weight: 0.0970 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.077006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.066732 restraints weight = 36517.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068283 restraints weight = 21083.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069384 restraints weight = 14305.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.070126 restraints weight = 10809.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.070475 restraints weight = 8831.146| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9770 Z= 0.142 Angle : 0.727 9.631 13276 Z= 0.353 Chirality : 0.044 0.149 1504 Planarity : 0.004 0.035 1640 Dihedral : 4.755 23.251 1284 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.25), residues: 1136 helix: 0.36 (0.19), residues: 784 sheet: -1.81 (1.13), residues: 18 loop : -2.65 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.025 0.002 TYR B 352 PHE 0.014 0.001 PHE A 549 TRP 0.023 0.002 TRP B 578 HIS 0.003 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9770) covalent geometry : angle 0.72694 (13276) hydrogen bonds : bond 0.04034 ( 472) hydrogen bonds : angle 4.09213 ( 1416) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 CYS cc_start: 0.7893 (m) cc_final: 0.7465 (m) REVERT: B 173 PHE cc_start: 0.8786 (m-80) cc_final: 0.8487 (m-80) REVERT: B 356 ASP cc_start: 0.8148 (p0) cc_final: 0.7941 (p0) REVERT: B 525 PHE cc_start: 0.8821 (m-80) cc_final: 0.8464 (m-80) REVERT: B 529 TRP cc_start: 0.8155 (t-100) cc_final: 0.7456 (t-100) REVERT: A 151 CYS cc_start: 0.7864 (m) cc_final: 0.7461 (m) REVERT: A 173 PHE cc_start: 0.8704 (m-80) cc_final: 0.8475 (m-80) REVERT: A 225 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8220 (mm-30) REVERT: A 297 ILE cc_start: 0.9027 (mm) cc_final: 0.8775 (mm) REVERT: A 529 TRP cc_start: 0.8180 (t-100) cc_final: 0.7433 (t-100) REVERT: A 570 LEU cc_start: 0.9418 (tp) cc_final: 0.9190 (tt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0765 time to fit residues: 15.4705 Evaluate side-chains 89 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 86 optimal weight: 0.0020 chunk 42 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.076431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.066199 restraints weight = 36593.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.067763 restraints weight = 21153.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068847 restraints weight = 14338.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069532 restraints weight = 10844.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070092 restraints weight = 8953.030| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9770 Z= 0.158 Angle : 0.737 10.389 13276 Z= 0.359 Chirality : 0.045 0.160 1504 Planarity : 0.004 0.034 1640 Dihedral : 4.767 21.475 1284 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.25), residues: 1136 helix: 0.36 (0.19), residues: 782 sheet: -1.90 (1.14), residues: 18 loop : -2.63 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 492 TYR 0.027 0.002 TYR B 352 PHE 0.018 0.001 PHE A 549 TRP 0.024 0.002 TRP B 578 HIS 0.003 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9770) covalent geometry : angle 0.73651 (13276) hydrogen bonds : bond 0.04075 ( 472) hydrogen bonds : angle 4.18231 ( 1416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1226.78 seconds wall clock time: 22 minutes 5.37 seconds (1325.37 seconds total)