Starting phenix.real_space_refine on Mon May 19 22:15:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w0p_43711/05_2025/8w0p_43711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w0p_43711/05_2025/8w0p_43711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w0p_43711/05_2025/8w0p_43711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w0p_43711/05_2025/8w0p_43711.map" model { file = "/net/cci-nas-00/data/ceres_data/8w0p_43711/05_2025/8w0p_43711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w0p_43711/05_2025/8w0p_43711.cif" } resolution = 3.26 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= 0.000 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 12249 2.51 5 N 3166 2.21 5 O 3673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19116 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 7573 Classifications: {'peptide': 916} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 887} Chain: "B" Number of atoms: 7592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 916, 7573 Classifications: {'peptide': 916} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 887} Conformer: "B" Number of residues, atoms: 916, 7573 Classifications: {'peptide': 916} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 887} bond proxies already assigned to first conformer: 7704 Chain: "C" Number of atoms: 3897 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 475, 3869 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 456} Conformer: "B" Number of residues, atoms: 475, 3869 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 456} bond proxies already assigned to first conformer: 3909 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS B 441 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 441 " occ=0.50 residue: pdb=" N AARG C 6 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 6 " occ=0.50 residue: pdb=" N AARG C 265 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 265 " occ=0.50 residue: pdb=" N ACYS C 282 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 282 " occ=0.50 Time building chain proxies: 15.57, per 1000 atoms: 0.81 Number of scatterers: 19116 At special positions: 0 Unit cell: (91.715, 158.613, 170.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 3673 8.00 N 3166 7.00 C 12249 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: 4.12 Conformation dependent library (CDL) restraints added in 3.6 seconds 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4388 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 26 sheets defined 50.4% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 4.163A pdb=" N ARG A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 62 removed outlier: 4.080A pdb=" N ILE A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.718A pdb=" N GLY A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.560A pdb=" N LYS A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.660A pdb=" N SER A 172 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 removed outlier: 3.671A pdb=" N ILE A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 253 removed outlier: 4.478A pdb=" N LEU A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 291 Processing helix chain 'A' and resid 295 through 302 removed outlier: 3.958A pdb=" N LYS A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 325 removed outlier: 4.178A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 322 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 removed outlier: 4.754A pdb=" N ILE A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 375 through 387 Processing helix chain 'A' and resid 401 through 416 removed outlier: 3.613A pdb=" N LYS A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 442 through 445 Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.560A pdb=" N TYR A 450 " --> pdb=" O TRP A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 446 through 450' Processing helix chain 'A' and resid 457 through 472 Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 549 through 552 Processing helix chain 'A' and resid 553 through 561 removed outlier: 3.806A pdb=" N TYR A 559 " --> pdb=" O ILE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 582 through 592 removed outlier: 3.588A pdb=" N LYS A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 606 removed outlier: 3.792A pdb=" N THR A 605 " --> pdb=" O PRO A 602 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE A 606 " --> pdb=" O GLN A 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 602 through 606' Processing helix chain 'A' and resid 623 through 658 removed outlier: 3.638A pdb=" N GLU A 640 " --> pdb=" O LYS A 636 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 656 " --> pdb=" O PHE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 676 Processing helix chain 'A' and resid 677 through 689 removed outlier: 3.862A pdb=" N ILE A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 700 Processing helix chain 'A' and resid 703 through 710 Processing helix chain 'A' and resid 710 through 718 removed outlier: 3.501A pdb=" N SER A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 742 removed outlier: 3.685A pdb=" N GLU A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 817 removed outlier: 3.587A pdb=" N SER A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 860 removed outlier: 4.289A pdb=" N ILE A 825 " --> pdb=" O GLU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 871 Processing helix chain 'A' and resid 875 through 883 Processing helix chain 'A' and resid 904 through 913 removed outlier: 3.592A pdb=" N GLU A 908 " --> pdb=" O LYS A 904 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 913 " --> pdb=" O ILE A 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 14 removed outlier: 3.690A pdb=" N ARG B 6 " --> pdb=" O LYS B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 62 removed outlier: 4.196A pdb=" N ILE B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 134 removed outlier: 3.949A pdb=" N LYS B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ALA B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 211 through 224 Processing helix chain 'B' and resid 232 through 253 removed outlier: 3.617A pdb=" N PHE B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 296 through 302 Processing helix chain 'B' and resid 312 through 323 removed outlier: 3.670A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.924A pdb=" N ARG B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 363 through 374 Processing helix chain 'B' and resid 375 through 388 Processing helix chain 'B' and resid 401 through 417 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 446 through 451 Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 535 through 540 removed outlier: 4.067A pdb=" N ARG B 539 " --> pdb=" O GLN B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 561 removed outlier: 3.826A pdb=" N GLU B 556 " --> pdb=" O ASN B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 582 through 592 removed outlier: 3.542A pdb=" N PHE B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 656 removed outlier: 3.559A pdb=" N TYR B 654 " --> pdb=" O ASP B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 675 Processing helix chain 'B' and resid 677 through 690 Processing helix chain 'B' and resid 694 through 700 removed outlier: 3.976A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASN B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 710 Processing helix chain 'B' and resid 710 through 718 Processing helix chain 'B' and resid 730 through 742 removed outlier: 3.818A pdb=" N GLU B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 816 removed outlier: 3.594A pdb=" N VAL B 785 " --> pdb=" O ASP B 781 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER B 788 " --> pdb=" O LYS B 784 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 789 " --> pdb=" O VAL B 785 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 860 removed outlier: 4.998A pdb=" N LYS B 824 " --> pdb=" O LYS B 820 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILE B 825 " --> pdb=" O GLU B 821 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 849 " --> pdb=" O SER B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 872 removed outlier: 4.282A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 883 Processing helix chain 'B' and resid 904 through 913 removed outlier: 3.583A pdb=" N GLU B 908 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 913 " --> pdb=" O ILE B 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.643A pdb=" N SER C 14 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU C 15 " --> pdb=" O PHE C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 42 removed outlier: 3.535A pdb=" N LEU C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.745A pdb=" N ARG C 82 " --> pdb=" O PHE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 95 removed outlier: 4.599A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS C 95 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 143 through 154 Processing helix chain 'C' and resid 155 through 162 Processing helix chain 'C' and resid 173 through 180 removed outlier: 3.531A pdb=" N ILE C 180 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 193 Processing helix chain 'C' and resid 193 through 215 Processing helix chain 'C' and resid 217 through 231 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 251 through 254 removed outlier: 3.577A pdb=" N SER C 254 " --> pdb=" O SER C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 254' Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.794A pdb=" N LEU C 316 " --> pdb=" O GLN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 399 removed outlier: 3.606A pdb=" N ALA C 394 " --> pdb=" O LYS C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 410 removed outlier: 3.856A pdb=" N TYR C 405 " --> pdb=" O PHE C 401 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 428 removed outlier: 4.032A pdb=" N LEU C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 476 removed outlier: 3.733A pdb=" N GLN C 452 " --> pdb=" O GLN C 448 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 75 removed outlier: 3.888A pdb=" N LYS A 74 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 89 " --> pdb=" O LYS A 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 80 Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 149 Processing sheet with id=AA6, first strand: chain 'A' and resid 478 through 479 removed outlier: 7.896A pdb=" N PHE A 479 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY A 453 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 393 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N CYS A 454 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP A 395 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASP A 518 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLY A 566 " --> pdb=" O LYS A 621 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 478 through 479 removed outlier: 7.896A pdb=" N PHE A 479 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY A 453 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 393 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N CYS A 454 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP A 395 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASP A 518 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLY A 566 " --> pdb=" O LYS A 621 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N THR A 614 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N SER A 600 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 616 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 598 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE A 618 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS A 596 " --> pdb=" O PRO A 745 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 503 through 504 Processing sheet with id=AA9, first strand: chain 'A' and resid 773 through 775 removed outlier: 7.301A pdb=" N ASP A 894 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB2, first strand: chain 'B' and resid 20 through 23 Processing sheet with id=AB3, first strand: chain 'B' and resid 70 through 71 removed outlier: 5.811A pdb=" N PHE B 101 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 142 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE B 103 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR B 144 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU B 105 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N VAL B 146 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 74 through 75 removed outlier: 3.901A pdb=" N LYS B 74 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 89 " --> pdb=" O LYS B 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 78 through 80 Processing sheet with id=AB6, first strand: chain 'B' and resid 393 through 394 removed outlier: 6.515A pdb=" N ASP B 518 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N GLY B 569 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 520 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL B 571 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N SER B 522 " --> pdb=" O VAL B 571 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY B 566 " --> pdb=" O LYS B 621 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN B 620 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL B 595 " --> pdb=" O GLN B 620 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LYS B 596 " --> pdb=" O PRO B 745 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 453 through 454 removed outlier: 6.441A pdb=" N GLY B 453 " --> pdb=" O PHE B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 503 through 504 Processing sheet with id=AB9, first strand: chain 'B' and resid 756 through 758 Processing sheet with id=AC1, first strand: chain 'B' and resid 861 through 862 Processing sheet with id=AC2, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 60 Processing sheet with id=AC4, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AC5, first strand: chain 'C' and resid 283 through 285 Processing sheet with id=AC6, first strand: chain 'C' and resid 290 through 295 removed outlier: 4.157A pdb=" N LEU C 347 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 308 through 310 removed outlier: 4.183A pdb=" N LYS C 328 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 352 through 353 857 hydrogen bonds defined for protein. 2453 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: 6.50 Time building geometry restraints manager: 4.87 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: 5733 1.34 - 1.45: 2871 1.45 - 1.57: 10850 1.57 - 1.69: 1 1.69 - 1.81: 51 Bond restraints: 19506 Sorted by residual: bond pdb=" C2 SAM B1001 " pdb=" N3 SAM B1001 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.48e+00 bond pdb=" C2 SAM A1001 " pdb=" N3 SAM A1001 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" C SER A 495 " pdb=" N PRO A 496 " ideal model delta sigma weight residual 1.330 1.363 -0.033 1.19e-02 7.06e+03 7.51e+00 bond pdb=" C8 SAM A1001 " pdb=" N7 SAM A1001 " ideal model delta sigma weight residual 1.298 1.352 -0.054 2.00e-02 2.50e+03 7.27e+00 bond pdb=" C8 SAM B1001 " pdb=" N7 SAM B1001 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.09e+00 ... (remaining 19501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 25701 1.76 - 3.52: 492 3.52 - 5.29: 79 5.29 - 7.05: 21 7.05 - 8.81: 9 Bond angle restraints: 26302 Sorted by residual: angle pdb=" N GLU C 456 " pdb=" CA GLU C 456 " pdb=" CB GLU C 456 " ideal model delta sigma weight residual 110.28 117.40 -7.12 1.55e+00 4.16e-01 2.11e+01 angle pdb=" C ILE C 455 " pdb=" N GLU C 456 " pdb=" CA GLU C 456 " ideal model delta sigma weight residual 120.31 113.36 6.95 1.52e+00 4.33e-01 2.09e+01 angle pdb=" C GLY B 509 " pdb=" N ASP B 510 " pdb=" CA ASP B 510 " ideal model delta sigma weight residual 125.66 133.62 -7.96 1.85e+00 2.92e-01 1.85e+01 angle pdb=" CA PRO A 273 " pdb=" N PRO A 273 " pdb=" CD PRO A 273 " ideal model delta sigma weight residual 112.00 106.15 5.85 1.40e+00 5.10e-01 1.74e+01 angle pdb=" CA PRO B 660 " pdb=" N PRO B 660 " pdb=" CD PRO B 660 " ideal model delta sigma weight residual 112.00 106.88 5.12 1.40e+00 5.10e-01 1.34e+01 ... (remaining 26297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 10624 17.71 - 35.41: 1032 35.41 - 53.12: 200 53.12 - 70.83: 47 70.83 - 88.54: 20 Dihedral angle restraints: 11923 sinusoidal: 5112 harmonic: 6811 Sorted by residual: dihedral pdb=" CA LEU B 288 " pdb=" C LEU B 288 " pdb=" N ARG B 289 " pdb=" CA ARG B 289 " ideal model delta harmonic sigma weight residual 180.00 156.71 23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA GLU A 346 " pdb=" C GLU A 346 " pdb=" N SER A 347 " pdb=" CA SER A 347 " ideal model delta harmonic sigma weight residual 180.00 157.32 22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ARG B 286 " pdb=" C ARG B 286 " pdb=" N ALA B 287 " pdb=" CA ALA B 287 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 11920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1890 0.036 - 0.073: 702 0.073 - 0.109: 202 0.109 - 0.145: 45 0.145 - 0.182: 7 Chirality restraints: 2846 Sorted by residual: chirality pdb=" C2' SAM A1001 " pdb=" C1' SAM A1001 " pdb=" C3' SAM A1001 " pdb=" O2' SAM A1001 " both_signs ideal model delta sigma weight residual False -2.76 -2.57 -0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" CB THR B 579 " pdb=" CA THR B 579 " pdb=" OG1 THR B 579 " pdb=" CG2 THR B 579 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" C2' SAM B1001 " pdb=" C1' SAM B1001 " pdb=" C3' SAM B1001 " pdb=" O2' SAM B1001 " both_signs ideal model delta sigma weight residual False -2.76 -2.58 -0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 2843 not shown) Planarity restraints: 3397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 272 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO A 273 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 273 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 273 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 659 " -0.054 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO B 660 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 660 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 660 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 311 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 312 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.028 5.00e-02 4.00e+02 ... (remaining 3394 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 547 2.71 - 3.25: 19744 3.25 - 3.80: 29427 3.80 - 4.35: 38531 4.35 - 4.90: 64025 Nonbonded interactions: 152274 Sorted by model distance: nonbonded pdb=" O GLY B 358 " pdb=" O3' SAM B1001 " model vdw 2.158 3.040 nonbonded pdb=" O PRO B 777 " pdb=" OH TYR B 861 " model vdw 2.175 3.040 nonbonded pdb=" O SER A 575 " pdb=" OG1 THR A 579 " model vdw 2.177 3.040 nonbonded pdb=" NH1 ARG A 586 " pdb=" O SER C 17 " model vdw 2.187 3.120 nonbonded pdb=" OH TYR C 60 " pdb=" O ASP C 97 " model vdw 2.191 3.040 ... (remaining 152269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 236 or resid 238 through 440 or resid 442 throug \ h 916 or resid 1001)) selection = (chain 'B' and (resid 1 through 236 or resid 238 through 440 or resid 442 throug \ h 916 or resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.260 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 47.670 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 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 : 0.003 0.089 19506 Z= 0.151 Angle : 0.626 8.809 26302 Z= 0.344 Chirality : 0.042 0.182 2846 Planarity : 0.004 0.115 3397 Dihedral : 14.727 88.535 7535 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.35 % Favored : 95.44 % Rotamer: Outliers : 0.14 % Allowed : 0.19 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.11 (0.17), residues: 2314 helix: 0.85 (0.17), residues: 984 sheet: -0.15 (0.34), residues: 229 loop : -0.87 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 665 HIS 0.005 0.001 HIS B 881 PHE 0.015 0.001 PHE A 882 TYR 0.020 0.001 TYR B 651 ARG 0.008 0.000 ARG C 244 Details of bonding type rmsd hydrogen bonds : bond 0.15499 ( 851) hydrogen bonds : angle 6.71380 ( 2453) covalent geometry : bond 0.00319 (19506) covalent geometry : angle 0.62635 (26302) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.3557 time to fit residues: 31.7651 Evaluate side-chains 29 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 92 optimal weight: 30.0000 chunk 179 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 133 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.111721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072018 restraints weight = 172094.800| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 9.16 r_work: 0.2798 rms_B_bonded: 7.56 restraints_weight: 2.0000 r_work: 0.2942 rms_B_bonded: 5.57 restraints_weight: 4.0000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 19506 Z= 0.240 Angle : 0.635 11.071 26302 Z= 0.338 Chirality : 0.044 0.210 2846 Planarity : 0.004 0.071 3397 Dihedral : 5.927 58.051 2593 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.74 % Favored : 95.09 % Rotamer: Outliers : 0.43 % Allowed : 4.13 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.10 (0.17), residues: 2314 helix: 1.03 (0.16), residues: 1010 sheet: -0.07 (0.34), residues: 228 loop : -0.80 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 665 HIS 0.010 0.001 HIS A 199 PHE 0.019 0.002 PHE C 22 TYR 0.038 0.002 TYR C 262 ARG 0.006 0.001 ARG B 659 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 851) hydrogen bonds : angle 5.03535 ( 2453) covalent geometry : bond 0.00557 (19506) covalent geometry : angle 0.63482 (26302) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 MET cc_start: 0.9489 (mmm) cc_final: 0.9224 (mmm) REVERT: B 438 MET cc_start: 0.8905 (mmm) cc_final: 0.8209 (mmm) outliers start: 6 outliers final: 3 residues processed: 35 average time/residue: 0.3387 time to fit residues: 21.4496 Evaluate side-chains 31 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 766 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 156 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 202 optimal weight: 0.9980 chunk 1 optimal weight: 0.0570 chunk 85 optimal weight: 3.9990 chunk 180 optimal weight: 0.0270 chunk 56 optimal weight: 0.6980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.113912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.074022 restraints weight = 199467.035| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 11.25 r_work: 0.2846 rms_B_bonded: 8.21 restraints_weight: 2.0000 r_work: 0.2919 rms_B_bonded: 7.17 restraints_weight: 4.0000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19506 Z= 0.105 Angle : 0.505 7.729 26302 Z= 0.272 Chirality : 0.041 0.172 2846 Planarity : 0.004 0.054 3397 Dihedral : 5.460 57.688 2593 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.04 % Favored : 95.78 % Rotamer: Outliers : 0.52 % Allowed : 5.79 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.37 (0.18), residues: 2314 helix: 1.34 (0.17), residues: 1010 sheet: 0.21 (0.35), residues: 224 loop : -0.78 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 665 HIS 0.003 0.001 HIS A 199 PHE 0.015 0.001 PHE C 22 TYR 0.032 0.001 TYR C 262 ARG 0.006 0.000 ARG B 659 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 851) hydrogen bonds : angle 4.50496 ( 2453) covalent geometry : bond 0.00224 (19506) covalent geometry : angle 0.50494 (26302) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9056 (mp) REVERT: A 468 MET cc_start: 0.9470 (mmm) cc_final: 0.9168 (mmm) REVERT: B 438 MET cc_start: 0.9148 (mmm) cc_final: 0.8489 (mmm) REVERT: B 468 MET cc_start: 0.8856 (ttp) cc_final: 0.8535 (ppp) REVERT: C 79 PHE cc_start: 0.8740 (m-80) cc_final: 0.8327 (m-80) REVERT: C 86 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8729 (t0) REVERT: C 337 MET cc_start: 0.8583 (mpp) cc_final: 0.8350 (mpp) outliers start: 8 outliers final: 4 residues processed: 41 average time/residue: 0.3155 time to fit residues: 22.9007 Evaluate side-chains 36 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 209 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 298 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 = 0.4123 r_free = 0.4123 target = 0.112624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072540 restraints weight = 179132.034| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 9.42 r_work: 0.2841 rms_B_bonded: 7.36 restraints_weight: 2.0000 r_work: 0.2962 rms_B_bonded: 5.51 restraints_weight: 4.0000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 19506 Z= 0.152 Angle : 0.524 10.402 26302 Z= 0.279 Chirality : 0.041 0.162 2846 Planarity : 0.003 0.046 3397 Dihedral : 5.538 59.321 2593 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.39 % Favored : 95.48 % Rotamer: Outliers : 0.81 % Allowed : 6.74 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.50 (0.18), residues: 2314 helix: 1.44 (0.17), residues: 1017 sheet: 0.26 (0.35), residues: 227 loop : -0.73 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 665 HIS 0.008 0.001 HIS A 199 PHE 0.015 0.001 PHE C 22 TYR 0.020 0.001 TYR C 24 ARG 0.004 0.000 ARG B 659 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 851) hydrogen bonds : angle 4.47889 ( 2453) covalent geometry : bond 0.00353 (19506) covalent geometry : angle 0.52355 (26302) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9403 (OUTLIER) cc_final: 0.9148 (mp0) REVERT: A 366 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9112 (mp) REVERT: A 468 MET cc_start: 0.9409 (mmm) cc_final: 0.9001 (mmm) REVERT: A 766 MET cc_start: 0.8739 (mpp) cc_final: 0.8524 (mpp) REVERT: B 438 MET cc_start: 0.9084 (mmm) cc_final: 0.8437 (mmm) REVERT: B 468 MET cc_start: 0.8795 (ttp) cc_final: 0.8411 (ppp) REVERT: C 337 MET cc_start: 0.8576 (mpp) cc_final: 0.8299 (mpp) REVERT: C 456 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8273 (pp20) outliers start: 14 outliers final: 5 residues processed: 43 average time/residue: 0.3261 time to fit residues: 23.6131 Evaluate side-chains 37 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 27 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 228 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 206 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.113212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.073121 restraints weight = 162739.367| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 8.95 r_work: 0.2854 rms_B_bonded: 7.92 restraints_weight: 2.0000 r_work: 0.2959 rms_B_bonded: 5.83 restraints_weight: 4.0000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 19506 Z= 0.112 Angle : 0.488 9.105 26302 Z= 0.262 Chirality : 0.040 0.158 2846 Planarity : 0.003 0.040 3397 Dihedral : 5.394 57.863 2593 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.22 % Favored : 95.65 % Rotamer: Outliers : 0.95 % Allowed : 7.17 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.55 (0.18), residues: 2314 helix: 1.52 (0.17), residues: 1019 sheet: 0.20 (0.35), residues: 228 loop : -0.72 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 665 HIS 0.004 0.001 HIS A 199 PHE 0.015 0.001 PHE A 345 TYR 0.017 0.001 TYR C 24 ARG 0.004 0.000 ARG B 659 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 851) hydrogen bonds : angle 4.32462 ( 2453) covalent geometry : bond 0.00252 (19506) covalent geometry : angle 0.48750 (26302) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.9130 (mp0) REVERT: A 366 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9065 (mp) REVERT: A 468 MET cc_start: 0.9449 (mmm) cc_final: 0.9108 (mmm) REVERT: B 438 MET cc_start: 0.9071 (mmm) cc_final: 0.8384 (mmm) REVERT: C 79 PHE cc_start: 0.8753 (m-80) cc_final: 0.8303 (m-80) REVERT: C 337 MET cc_start: 0.8581 (mpp) cc_final: 0.8322 (mpp) REVERT: C 456 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8200 (pp20) outliers start: 17 outliers final: 9 residues processed: 47 average time/residue: 0.3289 time to fit residues: 26.3623 Evaluate side-chains 42 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 659 ARG Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 14 optimal weight: 6.9990 chunk 216 optimal weight: 0.3980 chunk 137 optimal weight: 0.3980 chunk 154 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN ** C 86 ASN ** 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 = 0.4129 r_free = 0.4129 target = 0.113392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.071483 restraints weight = 191105.526| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 10.76 r_work: 0.2834 rms_B_bonded: 10.00 restraints_weight: 2.0000 r_work: 0.2917 rms_B_bonded: 8.38 restraints_weight: 4.0000 r_work: 0.3173 rms_B_bonded: 5.62 restraints_weight: 8.0000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 19506 Z= 0.105 Angle : 0.482 8.912 26302 Z= 0.258 Chirality : 0.040 0.152 2846 Planarity : 0.003 0.040 3397 Dihedral : 5.287 56.530 2593 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 1.09 % Allowed : 7.83 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.65 (0.18), residues: 2314 helix: 1.62 (0.17), residues: 1019 sheet: 0.24 (0.34), residues: 239 loop : -0.70 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 665 HIS 0.004 0.000 HIS A 199 PHE 0.016 0.001 PHE A 345 TYR 0.016 0.001 TYR C 24 ARG 0.004 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 851) hydrogen bonds : angle 4.20892 ( 2453) covalent geometry : bond 0.00236 (19506) covalent geometry : angle 0.48245 (26302) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 32 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9545 (OUTLIER) cc_final: 0.9258 (mp0) REVERT: A 366 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8927 (mp) REVERT: A 438 MET cc_start: 0.8765 (tpp) cc_final: 0.8482 (tpt) REVERT: A 468 MET cc_start: 0.9289 (mmm) cc_final: 0.8901 (mmm) REVERT: B 438 MET cc_start: 0.8838 (mmm) cc_final: 0.8226 (mmm) REVERT: C 79 PHE cc_start: 0.8721 (m-80) cc_final: 0.8272 (m-80) REVERT: C 337 MET cc_start: 0.8435 (mpp) cc_final: 0.8225 (mpp) outliers start: 20 outliers final: 9 residues processed: 50 average time/residue: 0.3394 time to fit residues: 28.0214 Evaluate side-chains 43 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 842 GLN Chi-restraints excluded: chain C residue 197 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 140 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 106 optimal weight: 6.9990 chunk 17 optimal weight: 0.0570 chunk 154 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.113408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.070429 restraints weight = 229984.754| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 12.68 r_work: 0.2850 rms_B_bonded: 11.31 restraints_weight: 2.0000 r_work: 0.2951 rms_B_bonded: 9.39 restraints_weight: 4.0000 r_work: 0.3131 rms_B_bonded: 8.43 restraints_weight: 8.0000 r_work: 0.3511 rms_B_bonded: 6.01 restraints_weight: 16.0000 r_work: 0.3979 rms_B_bonded: 5.02 restraints_weight: 32.0000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 19506 Z= 0.103 Angle : 0.482 8.531 26302 Z= 0.258 Chirality : 0.040 0.149 2846 Planarity : 0.003 0.040 3397 Dihedral : 5.250 56.426 2593 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.48 % Favored : 95.35 % Rotamer: Outliers : 0.90 % Allowed : 8.31 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.71 (0.18), residues: 2314 helix: 1.68 (0.17), residues: 1021 sheet: 0.23 (0.34), residues: 238 loop : -0.67 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 665 HIS 0.002 0.000 HIS A 199 PHE 0.014 0.001 PHE A 345 TYR 0.040 0.001 TYR C 262 ARG 0.004 0.000 ARG A 659 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 851) hydrogen bonds : angle 4.14712 ( 2453) covalent geometry : bond 0.00231 (19506) covalent geometry : angle 0.48216 (26302) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 2.216 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: A 346 GLU cc_start: 0.9666 (OUTLIER) cc_final: 0.9404 (mp0) REVERT: A 366 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8065 (mp) REVERT: A 438 MET cc_start: 0.8819 (tpp) cc_final: 0.8498 (tpt) REVERT: B 438 MET cc_start: 0.8691 (mmm) cc_final: 0.7864 (mmm) REVERT: B 908 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7635 (mp0) outliers start: 16 outliers final: 11 residues processed: 46 average time/residue: 0.3375 time to fit residues: 26.8639 Evaluate side-chains 43 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 430 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 19 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 37 optimal weight: 0.7980 chunk 215 optimal weight: 0.3980 chunk 199 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.113092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.072994 restraints weight = 159372.676| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 8.82 r_work: 0.2854 rms_B_bonded: 7.41 restraints_weight: 2.0000 r_work: 0.2930 rms_B_bonded: 6.32 restraints_weight: 4.0000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 19506 Z= 0.111 Angle : 0.487 8.415 26302 Z= 0.260 Chirality : 0.040 0.150 2846 Planarity : 0.003 0.041 3397 Dihedral : 5.253 56.319 2593 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.26 % Favored : 95.57 % Rotamer: Outliers : 0.95 % Allowed : 8.50 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.69 (0.18), residues: 2314 helix: 1.67 (0.17), residues: 1030 sheet: 0.06 (0.34), residues: 251 loop : -0.67 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 665 HIS 0.002 0.000 HIS A 199 PHE 0.014 0.001 PHE A 345 TYR 0.015 0.001 TYR C 24 ARG 0.009 0.000 ARG A 659 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 851) hydrogen bonds : angle 4.14040 ( 2453) covalent geometry : bond 0.00256 (19506) covalent geometry : angle 0.48664 (26302) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 30 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9452 (OUTLIER) cc_final: 0.9210 (mp0) REVERT: A 366 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9094 (mp) REVERT: A 659 ARG cc_start: 0.8278 (tmt170) cc_final: 0.8055 (tmt170) REVERT: B 438 MET cc_start: 0.9188 (mmm) cc_final: 0.8495 (mmm) REVERT: B 468 MET cc_start: 0.8722 (ttp) cc_final: 0.8408 (ppp) REVERT: B 908 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: C 337 MET cc_start: 0.8858 (mpp) cc_final: 0.8611 (mpp) outliers start: 17 outliers final: 12 residues processed: 45 average time/residue: 0.3283 time to fit residues: 25.4260 Evaluate side-chains 45 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 842 GLN Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 430 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 179 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 134 optimal weight: 0.0570 chunk 157 optimal weight: 0.0670 chunk 81 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.113307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.074688 restraints weight = 143876.294| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 7.70 r_work: 0.2911 rms_B_bonded: 6.63 restraints_weight: 2.0000 r_work: 0.2983 rms_B_bonded: 5.59 restraints_weight: 4.0000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 19506 Z= 0.099 Angle : 0.479 8.652 26302 Z= 0.255 Chirality : 0.040 0.147 2846 Planarity : 0.003 0.041 3397 Dihedral : 5.192 55.697 2593 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.26 % Favored : 95.57 % Rotamer: Outliers : 0.85 % Allowed : 8.83 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.71 (0.18), residues: 2314 helix: 1.71 (0.17), residues: 1027 sheet: 0.08 (0.33), residues: 251 loop : -0.67 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 665 HIS 0.002 0.000 HIS A 471 PHE 0.012 0.001 PHE C 22 TYR 0.014 0.001 TYR C 24 ARG 0.007 0.000 ARG A 659 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 851) hydrogen bonds : angle 4.09141 ( 2453) covalent geometry : bond 0.00221 (19506) covalent geometry : angle 0.47936 (26302) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9405 (OUTLIER) cc_final: 0.9184 (mp0) REVERT: A 366 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9040 (mp) REVERT: A 468 MET cc_start: 0.9350 (mmm) cc_final: 0.8818 (tmm) REVERT: A 659 ARG cc_start: 0.8337 (tmt170) cc_final: 0.8013 (tmt170) REVERT: B 438 MET cc_start: 0.9153 (mmm) cc_final: 0.8550 (mmm) REVERT: B 468 MET cc_start: 0.8716 (ttp) cc_final: 0.8452 (ppp) REVERT: B 908 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: C 337 MET cc_start: 0.8876 (mpp) cc_final: 0.8650 (mpp) outliers start: 15 outliers final: 11 residues processed: 45 average time/residue: 0.3254 time to fit residues: 25.2031 Evaluate side-chains 44 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 842 GLN Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.1037 > 50: distance: 75 - 80: 13.328 distance: 80 - 81: 12.505 distance: 81 - 82: 5.374 distance: 81 - 84: 9.492 distance: 82 - 83: 10.463 distance: 82 - 88: 22.124 distance: 82 - 98: 9.847 distance: 84 - 85: 12.821 distance: 85 - 86: 15.977 distance: 85 - 87: 45.567 distance: 88 - 89: 8.613 distance: 89 - 90: 16.493 distance: 89 - 92: 12.603 distance: 90 - 91: 29.685 distance: 90 - 108: 8.278 distance: 92 - 93: 5.076 distance: 93 - 94: 22.402 distance: 93 - 95: 26.245 distance: 94 - 96: 17.061 distance: 95 - 97: 17.015 distance: 96 - 97: 26.075 distance: 98 - 99: 12.983 distance: 99 - 100: 10.738 distance: 99 - 102: 19.102 distance: 100 - 101: 11.724 distance: 100 - 108: 22.254 distance: 102 - 103: 5.287 distance: 103 - 104: 4.993 distance: 103 - 105: 10.061 distance: 104 - 106: 8.990 distance: 105 - 107: 9.371 distance: 106 - 107: 8.269 distance: 108 - 109: 23.713 distance: 109 - 110: 12.216 distance: 109 - 112: 6.256 distance: 110 - 111: 23.574 distance: 110 - 116: 11.497 distance: 112 - 113: 9.767 distance: 113 - 114: 32.076 distance: 113 - 115: 11.933 distance: 116 - 117: 16.378 distance: 117 - 118: 9.745 distance: 117 - 120: 9.615 distance: 118 - 119: 6.103 distance: 118 - 125: 11.200 distance: 121 - 122: 15.459 distance: 122 - 123: 16.825 distance: 122 - 124: 8.717 distance: 125 - 126: 8.920 distance: 126 - 127: 4.908 distance: 126 - 129: 7.824 distance: 127 - 128: 31.876 distance: 127 - 133: 6.959 distance: 129 - 130: 4.510 distance: 130 - 131: 9.955 distance: 130 - 132: 18.093 distance: 133 - 134: 9.943 distance: 134 - 135: 8.552 distance: 134 - 137: 9.358 distance: 135 - 136: 4.623 distance: 135 - 142: 9.360 distance: 137 - 138: 13.895 distance: 138 - 139: 13.517 distance: 139 - 140: 16.697 distance: 140 - 141: 11.468 distance: 142 - 143: 8.737 distance: 143 - 144: 20.419 distance: 143 - 146: 23.914 distance: 144 - 145: 14.815 distance: 144 - 156: 24.281 distance: 145 - 181: 24.668 distance: 146 - 147: 7.944 distance: 147 - 148: 18.266 distance: 147 - 149: 19.699 distance: 148 - 150: 10.190 distance: 149 - 151: 6.779 distance: 149 - 152: 10.307 distance: 150 - 151: 8.743 distance: 151 - 153: 11.651 distance: 152 - 154: 12.637 distance: 153 - 155: 6.008 distance: 154 - 155: 10.738 distance: 156 - 157: 12.617 distance: 157 - 158: 21.790 distance: 157 - 160: 21.660 distance: 158 - 159: 16.590 distance: 158 - 161: 15.193 distance: 159 - 193: 12.733 distance: 161 - 162: 12.820 distance: 162 - 163: 15.346 distance: 162 - 165: 14.456 distance: 163 - 164: 10.097 distance: 165 - 166: 8.255 distance: 166 - 167: 3.255 distance: 167 - 168: 11.224 distance: 168 - 169: 9.124 distance: 169 - 170: 12.012 distance: 169 - 171: 13.329 distance: 172 - 173: 26.479 distance: 173 - 174: 19.915 distance: 173 - 176: 8.112 distance: 174 - 175: 14.439 distance: 174 - 181: 18.424 distance: 176 - 177: 12.234 distance: 177 - 178: 9.432 distance: 178 - 179: 22.678 distance: 178 - 180: 13.953