Starting phenix.real_space_refine on Fri Feb 14 00:02:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e0h_8948/02_2025/6e0h_8948_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e0h_8948/02_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_8948/02_2025/6e0h_8948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e0h_8948/02_2025/6e0h_8948.map" model { file = "/net/cci-nas-00/data/ceres_data/6e0h_8948/02_2025/6e0h_8948_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e0h_8948/02_2025/6e0h_8948_neut.cif" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9524 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" 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: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "A" 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: B Time building chain proxies: 9.38, per 1000 atoms: 0.98 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: 2.19 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.92 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: 2.68 Time building geometry restraints manager: 2.59 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.510 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.080 ------------------------------------------------------------------------------- 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= 0.565 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.033 0.004 TRP A 155 HIS 0.007 0.002 HIS A 619 PHE 0.031 0.003 PHE A 388 TYR 0.040 0.004 TYR A 352 ARG 0.006 0.001 ARG A 651 *********************** 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 : 1.041 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: 0.2945 time to fit residues: 89.7351 Evaluate side-chains 104 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.076419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.066019 restraints weight = 36346.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067540 restraints weight = 21376.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.068613 restraints weight = 14727.691| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9770 Z= 0.220 Angle : 0.754 10.587 13276 Z= 0.389 Chirality : 0.044 0.218 1504 Planarity : 0.006 0.046 1640 Dihedral : 5.888 28.005 1284 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.30 % Allowed : 3.47 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.21), residues: 1136 helix: -1.78 (0.15), residues: 776 sheet: -2.66 (1.07), residues: 22 loop : -3.54 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 578 HIS 0.002 0.001 HIS A 619 PHE 0.019 0.002 PHE B 549 TYR 0.045 0.002 TYR B 352 ARG 0.006 0.001 ARG A 427 *********************** 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 179 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 1.068 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: 0.7542 (m) cc_final: 0.7178 (m) REVERT: B 173 PHE cc_start: 0.8742 (m-80) cc_final: 0.8459 (m-80) REVERT: B 191 LEU cc_start: 0.9259 (tp) cc_final: 0.8959 (tp) REVERT: B 297 ILE cc_start: 0.9246 (mm) cc_final: 0.8818 (mm) REVERT: B 529 TRP cc_start: 0.8445 (t-100) cc_final: 0.8068 (t-100) REVERT: B 590 MET cc_start: 0.8629 (ptm) cc_final: 0.8151 (ttm) REVERT: A 151 CYS cc_start: 0.7541 (m) cc_final: 0.7129 (m) REVERT: A 173 PHE cc_start: 0.8695 (m-80) cc_final: 0.8171 (m-80) REVERT: A 191 LEU cc_start: 0.9236 (tp) cc_final: 0.8943 (tp) REVERT: A 297 ILE cc_start: 0.9240 (mm) cc_final: 0.8889 (mm) REVERT: A 352 TYR cc_start: 0.6320 (OUTLIER) cc_final: 0.5983 (m-80) REVERT: A 354 THR cc_start: 0.7792 (p) cc_final: 0.7234 (m) REVERT: A 502 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7999 (mt-10) REVERT: A 506 TYR cc_start: 0.8242 (t80) cc_final: 0.7907 (t80) REVERT: A 590 MET cc_start: 0.8618 (ptm) cc_final: 0.8125 (ttm) outliers start: 3 outliers final: 0 residues processed: 177 average time/residue: 0.1945 time to fit residues: 49.6852 Evaluate side-chains 106 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 115 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 68 optimal weight: 0.0370 chunk 26 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 54 optimal weight: 0.0370 chunk 63 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.076767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.066455 restraints weight = 36725.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.068011 restraints weight = 21177.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.069102 restraints weight = 14370.818| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3957 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= 0.190 Angle : 0.665 7.556 13276 Z= 0.341 Chirality : 0.043 0.133 1504 Planarity : 0.005 0.036 1640 Dihedral : 5.369 25.403 1284 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.23), residues: 1136 helix: -0.86 (0.17), residues: 778 sheet: -1.98 (1.10), residues: 22 loop : -3.23 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 578 HIS 0.002 0.000 HIS A 619 PHE 0.012 0.001 PHE A 367 TYR 0.021 0.002 TYR B 352 ARG 0.004 0.000 ARG A 496 *********************** 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 144 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.964 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: 0.7602 (m) cc_final: 0.7251 (m) REVERT: B 173 PHE cc_start: 0.8732 (m-80) cc_final: 0.8511 (m-80) REVERT: B 191 LEU cc_start: 0.9307 (tp) cc_final: 0.8939 (tp) REVERT: B 499 ASN cc_start: 0.7722 (m-40) cc_final: 0.7143 (m-40) REVERT: B 502 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7508 (mt-10) REVERT: B 529 TRP cc_start: 0.8400 (t-100) cc_final: 0.7836 (t-100) REVERT: B 590 MET cc_start: 0.8573 (ptm) cc_final: 0.8188 (ttm) REVERT: A 151 CYS cc_start: 0.7615 (m) cc_final: 0.7190 (m) REVERT: A 173 PHE cc_start: 0.8691 (m-80) cc_final: 0.8144 (m-80) REVERT: A 191 LEU cc_start: 0.9278 (tp) cc_final: 0.8932 (tp) REVERT: A 354 THR cc_start: 0.8456 (p) cc_final: 0.8027 (t) REVERT: A 499 ASN cc_start: 0.7657 (m-40) cc_final: 0.6670 (m-40) REVERT: A 502 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8110 (mt-10) REVERT: A 506 TYR cc_start: 0.8190 (t80) cc_final: 0.7943 (t80) REVERT: A 529 TRP cc_start: 0.8379 (t-100) cc_final: 0.8173 (t-100) REVERT: A 570 LEU cc_start: 0.9510 (tp) cc_final: 0.9231 (tt) REVERT: A 590 MET cc_start: 0.8626 (ptm) cc_final: 0.8190 (ttm) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2140 time to fit residues: 43.7304 Evaluate side-chains 108 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 69 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 109 optimal weight: 0.4980 chunk 2 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 = 0.3231 r_free = 0.3231 target = 0.072868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.062472 restraints weight = 37588.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.064007 restraints weight = 21858.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.065045 restraints weight = 14932.161| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9770 Z= 0.382 Angle : 0.771 8.719 13276 Z= 0.397 Chirality : 0.047 0.166 1504 Planarity : 0.005 0.034 1640 Dihedral : 5.391 26.560 1284 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.24), residues: 1136 helix: -0.37 (0.18), residues: 764 sheet: -2.07 (1.05), residues: 22 loop : -3.03 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 578 HIS 0.006 0.001 HIS B 619 PHE 0.018 0.002 PHE B 61 TYR 0.030 0.002 TYR A 352 ARG 0.007 0.001 ARG A 276 *********************** 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 131 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.154 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: 0.7732 (m) cc_final: 0.7331 (m) REVERT: B 191 LEU cc_start: 0.9463 (tp) cc_final: 0.9252 (tp) REVERT: B 354 THR cc_start: 0.8444 (t) cc_final: 0.8048 (m) REVERT: B 529 TRP cc_start: 0.8431 (t-100) cc_final: 0.7741 (t-100) REVERT: B 564 ASP cc_start: 0.8093 (t70) cc_final: 0.7740 (t0) REVERT: B 590 MET cc_start: 0.8600 (ptm) cc_final: 0.8281 (ttm) REVERT: A 151 CYS cc_start: 0.7889 (m) cc_final: 0.7435 (m) REVERT: A 173 PHE cc_start: 0.8727 (m-80) cc_final: 0.8371 (m-80) REVERT: A 354 THR cc_start: 0.7958 (p) cc_final: 0.7652 (p) REVERT: A 499 ASN cc_start: 0.7661 (m-40) cc_final: 0.6847 (m-40) REVERT: A 502 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8135 (mt-10) REVERT: A 529 TRP cc_start: 0.8514 (t-100) cc_final: 0.7880 (t-100) REVERT: A 570 LEU cc_start: 0.9585 (tp) cc_final: 0.9327 (tt) REVERT: A 590 MET cc_start: 0.8596 (ptm) cc_final: 0.8173 (ttm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2101 time to fit residues: 39.3832 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 : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS B 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.076251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.066083 restraints weight = 36680.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.067618 restraints weight = 20922.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.068682 restraints weight = 14262.236| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4460 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= 0.195 Angle : 0.689 7.771 13276 Z= 0.341 Chirality : 0.043 0.178 1504 Planarity : 0.004 0.034 1640 Dihedral : 5.102 24.869 1284 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.24), residues: 1136 helix: -0.00 (0.18), residues: 776 sheet: -1.63 (1.20), residues: 18 loop : -3.06 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 578 HIS 0.004 0.001 HIS B 113 PHE 0.039 0.002 PHE A 525 TYR 0.020 0.002 TYR A 352 ARG 0.007 0.000 ARG A 74 *********************** 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 141 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.053 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: 0.7346 (m) cc_final: 0.6985 (m) REVERT: B 173 PHE cc_start: 0.8754 (m-80) cc_final: 0.8551 (m-80) REVERT: B 191 LEU cc_start: 0.9433 (tp) cc_final: 0.9231 (tp) REVERT: B 529 TRP cc_start: 0.8138 (t-100) cc_final: 0.7333 (t-100) REVERT: B 578 TRP cc_start: 0.8273 (t-100) cc_final: 0.8033 (t60) REVERT: B 590 MET cc_start: 0.8514 (ptm) cc_final: 0.8209 (ttm) REVERT: A 151 CYS cc_start: 0.7633 (m) cc_final: 0.7233 (m) REVERT: A 173 PHE cc_start: 0.8699 (m-80) cc_final: 0.8224 (m-80) REVERT: A 529 TRP cc_start: 0.8229 (t-100) cc_final: 0.7459 (t-100) REVERT: A 570 LEU cc_start: 0.9482 (tp) cc_final: 0.9204 (tt) REVERT: A 590 MET cc_start: 0.8503 (ptm) cc_final: 0.8093 (ttm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1980 time to fit residues: 40.7741 Evaluate side-chains 97 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN B 518 GLN B 540 ASN A 113 HIS A 499 ASN A 518 GLN A 540 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.076783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.066526 restraints weight = 36765.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068093 restraints weight = 20974.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069170 restraints weight = 14137.854| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4745 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= 0.183 Angle : 0.684 7.748 13276 Z= 0.337 Chirality : 0.043 0.153 1504 Planarity : 0.004 0.039 1640 Dihedral : 4.874 23.010 1284 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.25), residues: 1136 helix: 0.23 (0.19), residues: 778 sheet: -1.29 (1.26), residues: 18 loop : -2.96 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 578 HIS 0.003 0.001 HIS B 619 PHE 0.025 0.001 PHE A 525 TYR 0.027 0.002 TYR B 352 ARG 0.005 0.000 ARG A 74 *********************** 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 131 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.149 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: 0.8823 (mm-40) cc_final: 0.8578 (tp-100) REVERT: B 151 CYS cc_start: 0.7780 (m) cc_final: 0.7262 (m) REVERT: B 173 PHE cc_start: 0.8754 (m-80) cc_final: 0.8498 (m-80) REVERT: B 354 THR cc_start: 0.8180 (t) cc_final: 0.7960 (m) REVERT: B 457 ARG cc_start: 0.8247 (ttt180) cc_final: 0.7978 (ptm-80) REVERT: B 529 TRP cc_start: 0.8100 (t-100) cc_final: 0.7502 (t-100) REVERT: B 590 MET cc_start: 0.8514 (ptm) cc_final: 0.8182 (ttm) REVERT: A 40 LEU cc_start: 0.9048 (mt) cc_final: 0.8825 (mt) REVERT: A 151 CYS cc_start: 0.7626 (m) cc_final: 0.7233 (m) REVERT: A 173 PHE cc_start: 0.8704 (m-80) cc_final: 0.8222 (m-80) REVERT: A 225 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8116 (mm-30) REVERT: A 354 THR cc_start: 0.8312 (t) cc_final: 0.8078 (m) REVERT: A 502 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8030 (mt-10) REVERT: A 529 TRP cc_start: 0.8210 (t-100) cc_final: 0.7442 (t-100) REVERT: A 570 LEU cc_start: 0.9400 (tp) cc_final: 0.9156 (tt) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1929 time to fit residues: 37.4219 Evaluate side-chains 95 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 60 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS B 639 ASN ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS A 540 ASN A 639 ASN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.064280 restraints weight = 37435.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.065864 restraints weight = 21396.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.066908 restraints weight = 14494.291| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9770 Z= 0.256 Angle : 0.718 8.706 13276 Z= 0.359 Chirality : 0.045 0.167 1504 Planarity : 0.004 0.035 1640 Dihedral : 4.930 24.116 1284 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.25), residues: 1136 helix: 0.24 (0.19), residues: 780 sheet: -1.87 (1.07), residues: 22 loop : -2.88 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 578 HIS 0.004 0.001 HIS B 619 PHE 0.021 0.002 PHE B 525 TYR 0.026 0.002 TYR B 352 ARG 0.004 0.000 ARG A 74 *********************** 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 121 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 CYS cc_start: 0.7844 (m) cc_final: 0.7399 (m) REVERT: B 191 LEU cc_start: 0.9414 (tp) cc_final: 0.9196 (tp) REVERT: B 529 TRP cc_start: 0.8185 (t-100) cc_final: 0.7529 (t-100) REVERT: B 590 MET cc_start: 0.8520 (ptm) cc_final: 0.8257 (ttm) REVERT: A 151 CYS cc_start: 0.7981 (m) cc_final: 0.7493 (m) REVERT: A 173 PHE cc_start: 0.8742 (m-80) cc_final: 0.8291 (m-80) REVERT: A 502 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8042 (mt-10) REVERT: A 529 TRP cc_start: 0.8299 (t-100) cc_final: 0.7470 (t-100) REVERT: A 570 LEU cc_start: 0.9422 (tp) cc_final: 0.9192 (tt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1794 time to fit residues: 32.8722 Evaluate side-chains 92 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 54 optimal weight: 0.0870 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.3271 r_free = 0.3271 target = 0.074839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.064435 restraints weight = 37693.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.066001 restraints weight = 21622.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.066989 restraints weight = 14737.839| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4869 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= 0.266 Angle : 0.728 8.294 13276 Z= 0.363 Chirality : 0.046 0.187 1504 Planarity : 0.004 0.036 1640 Dihedral : 4.991 23.619 1284 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.25), residues: 1136 helix: 0.26 (0.19), residues: 776 sheet: -1.75 (1.18), residues: 18 loop : -2.80 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 578 HIS 0.004 0.001 HIS B 619 PHE 0.025 0.002 PHE B 525 TYR 0.028 0.002 TYR B 352 ARG 0.004 0.000 ARG A 74 *********************** 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 122 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLU cc_start: 0.9321 (mp0) cc_final: 0.9056 (mp0) REVERT: B 151 CYS cc_start: 0.7832 (m) cc_final: 0.7301 (m) REVERT: B 191 LEU cc_start: 0.9412 (tp) cc_final: 0.9200 (tp) REVERT: B 529 TRP cc_start: 0.8248 (t-100) cc_final: 0.7558 (t-100) REVERT: A 151 CYS cc_start: 0.7967 (m) cc_final: 0.7625 (m) REVERT: A 173 PHE cc_start: 0.8718 (m-80) cc_final: 0.8312 (m-80) REVERT: A 570 LEU cc_start: 0.9417 (tp) cc_final: 0.9204 (tt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1816 time to fit residues: 33.5993 Evaluate side-chains 88 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 ASN ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.3263 r_free = 0.3263 target = 0.074520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064049 restraints weight = 37244.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.065591 restraints weight = 21609.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.066682 restraints weight = 14826.132| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9770 Z= 0.271 Angle : 0.734 9.391 13276 Z= 0.366 Chirality : 0.045 0.165 1504 Planarity : 0.004 0.036 1640 Dihedral : 5.028 24.344 1284 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.25), residues: 1136 helix: 0.35 (0.19), residues: 774 sheet: -2.05 (1.14), residues: 18 loop : -2.80 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 578 HIS 0.004 0.001 HIS B 619 PHE 0.023 0.002 PHE B 525 TYR 0.043 0.002 TYR B 352 ARG 0.004 0.000 ARG A 74 *********************** 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 121 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.099 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 42 GLU cc_start: 0.9229 (mp0) cc_final: 0.8881 (mp0) REVERT: B 151 CYS cc_start: 0.7793 (m) cc_final: 0.7302 (m) REVERT: B 191 LEU cc_start: 0.9413 (tp) cc_final: 0.9118 (tp) REVERT: B 225 GLU cc_start: 0.7933 (mp0) cc_final: 0.7352 (mp0) REVERT: B 506 TYR cc_start: 0.8460 (t80) cc_final: 0.8228 (t80) REVERT: A 42 GLU cc_start: 0.9272 (mp0) cc_final: 0.9059 (mp0) REVERT: A 151 CYS cc_start: 0.7984 (m) cc_final: 0.7476 (m) REVERT: A 173 PHE cc_start: 0.8713 (m-80) cc_final: 0.8316 (m-80) REVERT: A 570 LEU cc_start: 0.9392 (tp) cc_final: 0.9167 (tt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1897 time to fit residues: 34.0679 Evaluate side-chains 91 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 44 optimal weight: 0.1980 chunk 7 optimal weight: 0.0020 chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 97 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 518 GLN B 540 ASN ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.077644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067315 restraints weight = 36549.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.068939 restraints weight = 20994.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070033 restraints weight = 14161.303| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9770 Z= 0.175 Angle : 0.703 9.877 13276 Z= 0.345 Chirality : 0.043 0.184 1504 Planarity : 0.004 0.038 1640 Dihedral : 4.786 22.269 1284 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.25), residues: 1136 helix: 0.47 (0.19), residues: 764 sheet: -1.64 (1.25), residues: 18 loop : -2.74 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 133 HIS 0.002 0.001 HIS B 619 PHE 0.025 0.001 PHE B 525 TYR 0.051 0.001 TYR B 352 ARG 0.004 0.000 ARG A 74 ********************** 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 : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLU cc_start: 0.9224 (mp0) cc_final: 0.9019 (mp0) REVERT: B 151 CYS cc_start: 0.7744 (m) cc_final: 0.7327 (m) REVERT: B 173 PHE cc_start: 0.8764 (m-80) cc_final: 0.8447 (m-80) REVERT: B 191 LEU cc_start: 0.9359 (tp) cc_final: 0.9135 (tp) REVERT: B 274 THR cc_start: 0.8745 (p) cc_final: 0.8048 (m) REVERT: B 354 THR cc_start: 0.8375 (m) cc_final: 0.8151 (m) REVERT: B 529 TRP cc_start: 0.8064 (t-100) cc_final: 0.7209 (t-100) REVERT: A 151 CYS cc_start: 0.7875 (m) cc_final: 0.7418 (m) REVERT: A 173 PHE cc_start: 0.8626 (m-80) cc_final: 0.8415 (m-80) REVERT: A 225 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8083 (mm-30) REVERT: A 274 THR cc_start: 0.8831 (p) cc_final: 0.8171 (m) REVERT: A 570 LEU cc_start: 0.9339 (tp) cc_final: 0.9110 (tt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1824 time to fit residues: 36.8135 Evaluate side-chains 96 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 101 optimal weight: 0.0570 chunk 88 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS B 540 ASN ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.077640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.067232 restraints weight = 36370.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068819 restraints weight = 20948.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.069907 restraints weight = 14262.124| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5329 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= 0.195 Angle : 0.714 10.050 13276 Z= 0.350 Chirality : 0.044 0.204 1504 Planarity : 0.004 0.037 1640 Dihedral : 4.707 21.331 1284 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.25), residues: 1136 helix: 0.48 (0.19), residues: 764 sheet: -1.65 (1.23), residues: 18 loop : -2.67 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 578 HIS 0.003 0.001 HIS B 113 PHE 0.026 0.001 PHE B 525 TYR 0.039 0.002 TYR B 352 ARG 0.005 0.000 ARG A 492 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2397.12 seconds wall clock time: 44 minutes 15.85 seconds (2655.85 seconds total)