Starting phenix.real_space_refine on Fri Aug 9 09:39:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/08_2024/7sto_25435_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/08_2024/7sto_25435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/08_2024/7sto_25435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/08_2024/7sto_25435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/08_2024/7sto_25435_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sto_25435/08_2024/7sto_25435_trim.cif" } resolution = 3.15 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= 0.002 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 56 5.16 5 C 8478 2.51 5 N 2064 2.21 5 O 2336 1.98 5 H 12268 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25210 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 12410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12410 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 24, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 12410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12410 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 24, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 158 Unusual residues: {'3PE': 3, 'BJ9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 232 Unusual residues: {'3PE': 5, 'BJ9': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 Time building chain proxies: 11.23, per 1000 atoms: 0.45 Number of scatterers: 25210 At special positions: 0 Unit cell: (93.96, 126.36, 119.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 8 15.00 O 2336 8.00 N 2064 7.00 C 8478 6.00 H 12268 1.00 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 - 3.50 Amino acid : False - 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: 18.49 Conformation dependent library (CDL) restraints added in 2.4 seconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 6 sheets defined 60.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'B' and resid 147 through 155 removed outlier: 3.571A pdb=" N ARG B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.750A pdb=" N PHE B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.611A pdb=" N TYR B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 343 Processing helix chain 'B' and resid 352 through 355 removed outlier: 3.656A pdb=" N LYS B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 370 through 381 Processing helix chain 'B' and resid 439 through 451 removed outlier: 3.835A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 444 " --> pdb=" O LYS B 440 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 451 " --> pdb=" O TRP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 457 removed outlier: 3.563A pdb=" N VAL B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 485 removed outlier: 3.871A pdb=" N ASP B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 532 removed outlier: 4.791A pdb=" N LYS B 525 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Proline residue: B 526 - end of helix Processing helix chain 'B' and resid 545 through 550 removed outlier: 3.572A pdb=" N LEU B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN B 550 " --> pdb=" O PHE B 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 545 through 550' Processing helix chain 'B' and resid 557 through 569 removed outlier: 4.044A pdb=" N GLY B 565 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 590 Processing helix chain 'B' and resid 593 through 598 Processing helix chain 'B' and resid 599 through 602 Processing helix chain 'B' and resid 603 through 613 removed outlier: 4.386A pdb=" N LEU B 607 " --> pdb=" O GLU B 603 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS B 608 " --> pdb=" O ASP B 604 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 609 " --> pdb=" O ARG B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 661 removed outlier: 4.071A pdb=" N ARG B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP B 647 " --> pdb=" O GLN B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 667 removed outlier: 3.519A pdb=" N VAL B 665 " --> pdb=" O PHE B 662 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 667 " --> pdb=" O LYS B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 694 Processing helix chain 'B' and resid 694 through 710 removed outlier: 3.581A pdb=" N LEU B 710 " --> pdb=" O LEU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 745 Processing helix chain 'B' and resid 750 through 787 removed outlier: 3.943A pdb=" N TYR B 754 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 787 " --> pdb=" O ILE B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 798 Processing helix chain 'B' and resid 798 through 822 removed outlier: 3.948A pdb=" N ALA B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 831 Processing helix chain 'B' and resid 831 through 853 Proline residue: B 840 - end of helix removed outlier: 3.821A pdb=" N LEU B 846 " --> pdb=" O TYR B 842 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN B 847 " --> pdb=" O VAL B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 904 Processing helix chain 'B' and resid 917 through 946 removed outlier: 4.195A pdb=" N TYR B 921 " --> pdb=" O ASN B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 954 removed outlier: 4.160A pdb=" N ASN B 951 " --> pdb=" O GLY B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 1002 removed outlier: 4.008A pdb=" N ASN B 961 " --> pdb=" O THR B 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.571A pdb=" N ARG A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.749A pdb=" N PHE A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.611A pdb=" N TYR A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 343 Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.656A pdb=" N LYS A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.835A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 451 " --> pdb=" O TRP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 removed outlier: 3.563A pdb=" N VAL A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 removed outlier: 3.870A pdb=" N ASP A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 532 removed outlier: 4.791A pdb=" N LYS A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Proline residue: A 526 - end of helix Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.573A pdb=" N LEU A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 545 through 550' Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.043A pdb=" N GLY A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 599 through 602 Processing helix chain 'A' and resid 603 through 613 removed outlier: 4.385A pdb=" N LEU A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 609 " --> pdb=" O ARG A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 661 removed outlier: 4.071A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 667 removed outlier: 3.519A pdb=" N VAL A 665 " --> pdb=" O PHE A 662 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 667 " --> pdb=" O LYS A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 694 Processing helix chain 'A' and resid 694 through 710 removed outlier: 3.581A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 745 Processing helix chain 'A' and resid 750 through 787 removed outlier: 3.944A pdb=" N TYR A 754 " --> pdb=" O THR A 750 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY A 787 " --> pdb=" O ILE A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 798 Processing helix chain 'A' and resid 798 through 822 removed outlier: 3.948A pdb=" N ALA A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 831 Processing helix chain 'A' and resid 831 through 853 Proline residue: A 840 - end of helix removed outlier: 3.821A pdb=" N LEU A 846 " --> pdb=" O TYR A 842 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN A 847 " --> pdb=" O VAL A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 904 Processing helix chain 'A' and resid 917 through 946 removed outlier: 4.196A pdb=" N TYR A 921 " --> pdb=" O ASN A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 954 removed outlier: 4.159A pdb=" N ASN A 951 " --> pdb=" O GLY A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 1002 removed outlier: 4.008A pdb=" N ASN A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 239 through 240 removed outlier: 3.844A pdb=" N LYS A 874 " --> pdb=" O ASP A 882 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG B 391 " --> pdb=" O ALA A 873 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU A 875 " --> pdb=" O ARG B 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 248 through 252 removed outlier: 7.885A pdb=" N PHE B 279 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N THR B 405 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE B 357 " --> pdb=" O GLN B 429 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU B 431 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL B 359 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N CYS B 433 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 361 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS B 435 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER B 363 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET B 313 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 464 " --> pdb=" O MET B 313 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 315 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE B 541 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY B 493 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ARG B 622 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 491 " --> pdb=" O ARG B 622 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N CYS B 624 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY B 493 " --> pdb=" O CYS B 624 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N SER B 626 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N ILE B 495 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N ARG B 628 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N THR B 497 " --> pdb=" O ARG B 628 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLU B 630 " --> pdb=" O THR B 497 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 409 through 413 removed outlier: 7.174A pdb=" N LYS B 419 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.844A pdb=" N LYS B 874 " --> pdb=" O ASP B 882 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 252 removed outlier: 7.885A pdb=" N PHE A 279 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N THR A 405 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE A 357 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU A 431 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A 359 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N CYS A 433 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 361 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS A 435 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER A 363 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET A 313 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU A 464 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 315 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE A 541 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 493 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ARG A 622 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA A 491 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N CYS A 624 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY A 493 " --> pdb=" O CYS A 624 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N SER A 626 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N ILE A 495 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N ARG A 628 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N THR A 497 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLU A 630 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 413 removed outlier: 7.173A pdb=" N LYS A 419 " --> pdb=" O SER A 411 " (cutoff:3.500A) 721 hydrogen bonds defined for protein. 2079 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: 9.93 Time building geometry restraints manager: 19.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12244 1.03 - 1.22: 48 1.22 - 1.42: 5650 1.42 - 1.61: 7472 1.61 - 1.81: 104 Bond restraints: 25518 Sorted by residual: bond pdb=" C19 BJ9 B1204 " pdb=" N18 BJ9 B1204 " ideal model delta sigma weight residual 1.332 1.492 -0.160 2.00e-02 2.50e+03 6.43e+01 bond pdb=" C19 BJ9 A1205 " pdb=" N18 BJ9 A1205 " ideal model delta sigma weight residual 1.332 1.492 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" C06 BJ9 A1205 " pdb=" N05 BJ9 A1205 " ideal model delta sigma weight residual 1.365 1.523 -0.158 2.00e-02 2.50e+03 6.27e+01 bond pdb=" C06 BJ9 B1204 " pdb=" N05 BJ9 B1204 " ideal model delta sigma weight residual 1.365 1.522 -0.157 2.00e-02 2.50e+03 6.20e+01 bond pdb=" C06 BJ9 B1204 " pdb=" N08 BJ9 B1204 " ideal model delta sigma weight residual 1.381 1.537 -0.156 2.00e-02 2.50e+03 6.10e+01 ... (remaining 25513 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.03: 383 107.03 - 113.79: 29200 113.79 - 120.55: 9450 120.55 - 127.30: 6525 127.30 - 134.06: 130 Bond angle restraints: 45688 Sorted by residual: angle pdb=" CA THR B 947 " pdb=" C THR B 947 " pdb=" O THR B 947 " ideal model delta sigma weight residual 120.24 114.36 5.88 1.11e+00 8.12e-01 2.81e+01 angle pdb=" CA THR A 947 " pdb=" C THR A 947 " pdb=" O THR A 947 " ideal model delta sigma weight residual 120.24 114.39 5.85 1.11e+00 8.12e-01 2.78e+01 angle pdb=" O12 3PE B1202 " pdb=" P 3PE B1202 " pdb=" O14 3PE B1202 " ideal model delta sigma weight residual 123.79 109.61 14.18 3.00e+00 1.11e-01 2.23e+01 angle pdb=" O12 3PE A1202 " pdb=" P 3PE A1202 " pdb=" O14 3PE A1202 " ideal model delta sigma weight residual 123.79 109.66 14.13 3.00e+00 1.11e-01 2.22e+01 angle pdb=" O12 3PE A1204 " pdb=" P 3PE A1204 " pdb=" O14 3PE A1204 " ideal model delta sigma weight residual 123.79 109.71 14.08 3.00e+00 1.11e-01 2.20e+01 ... (remaining 45683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 11594 17.78 - 35.56: 482 35.56 - 53.34: 178 53.34 - 71.12: 62 71.12 - 88.91: 10 Dihedral angle restraints: 12326 sinusoidal: 6564 harmonic: 5762 Sorted by residual: dihedral pdb=" O21 3PE B1202 " pdb=" C2 3PE B1202 " pdb=" C3 3PE B1202 " pdb=" O31 3PE B1202 " ideal model delta sinusoidal sigma weight residual 60.47 -23.68 84.15 1 3.00e+01 1.11e-03 9.58e+00 dihedral pdb=" O21 3PE A1202 " pdb=" C2 3PE A1202 " pdb=" C3 3PE A1202 " pdb=" O31 3PE A1202 " ideal model delta sinusoidal sigma weight residual 60.47 -23.65 84.12 1 3.00e+01 1.11e-03 9.57e+00 dihedral pdb=" O21 3PE B1201 " pdb=" C2 3PE B1201 " pdb=" C3 3PE B1201 " pdb=" O31 3PE B1201 " ideal model delta sinusoidal sigma weight residual 60.47 -23.12 83.59 1 3.00e+01 1.11e-03 9.48e+00 ... (remaining 12323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1742 0.062 - 0.125: 208 0.125 - 0.187: 16 0.187 - 0.250: 6 0.250 - 0.312: 2 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C10 BJ9 B1204 " pdb=" C09 BJ9 B1204 " pdb=" C11 BJ9 B1204 " pdb=" O33 BJ9 B1204 " both_signs ideal model delta sigma weight residual False -2.47 -2.78 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C10 BJ9 A1205 " pdb=" C09 BJ9 A1205 " pdb=" C11 BJ9 A1205 " pdb=" O33 BJ9 A1205 " both_signs ideal model delta sigma weight residual False -2.47 -2.77 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ILE B 790 " pdb=" N ILE B 790 " pdb=" C ILE B 790 " pdb=" CB ILE B 790 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1971 not shown) Planarity restraints: 3742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 785 " -0.014 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" N SER A 786 " 0.045 2.00e-02 2.50e+03 pdb=" CA SER A 786 " -0.012 2.00e-02 2.50e+03 pdb=" H SER A 786 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 785 " 0.014 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" N SER B 786 " -0.045 2.00e-02 2.50e+03 pdb=" CA SER B 786 " 0.012 2.00e-02 2.50e+03 pdb=" H SER B 786 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 788 " 0.011 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" N ARG B 789 " -0.034 2.00e-02 2.50e+03 pdb=" CA ARG B 789 " 0.009 2.00e-02 2.50e+03 pdb=" H ARG B 789 " 0.014 2.00e-02 2.50e+03 ... (remaining 3739 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 2891 2.27 - 2.85: 56098 2.85 - 3.43: 63297 3.43 - 4.02: 87202 4.02 - 4.60: 137107 Nonbonded interactions: 346595 Sorted by model distance: nonbonded pdb=" O TRP A 666 " pdb=" HZ3 LYS A 675 " model vdw 1.685 2.450 nonbonded pdb=" O TRP B 666 " pdb=" HZ3 LYS B 675 " model vdw 1.686 2.450 nonbonded pdb=" O GLU B 256 " pdb=" HG SER B 259 " model vdw 1.689 2.450 nonbonded pdb=" O GLU A 256 " pdb=" HG SER A 259 " model vdw 1.689 2.450 nonbonded pdb=" O GLY B 593 " pdb=" HG SER B 597 " model vdw 1.709 2.450 ... (remaining 346590 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 135 through 1002 or resid 1201 through 1203)) selection = (chain 'B' and (resid 135 through 1002 or resid 1201 through 1203)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.410 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 77.320 Find NCS groups from input model: 0.820 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: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.007 0.160 13250 Z= 0.419 Angle : 0.878 14.180 17906 Z= 0.390 Chirality : 0.043 0.312 1974 Planarity : 0.003 0.023 2218 Dihedral : 11.851 88.905 4944 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.15 % Allowed : 1.51 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.21), residues: 1564 helix: 2.70 (0.18), residues: 816 sheet: 0.98 (0.46), residues: 140 loop : -0.73 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 933 HIS 0.004 0.001 HIS A 670 PHE 0.019 0.001 PHE B 261 TYR 0.011 0.001 TYR B 517 ARG 0.008 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.841 Fit side-chains REVERT: B 496 THR cc_start: 0.8567 (m) cc_final: 0.8359 (p) REVERT: B 699 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: A 496 THR cc_start: 0.8560 (m) cc_final: 0.8348 (p) REVERT: A 699 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.8248 (m-80) outliers start: 2 outliers final: 0 residues processed: 132 average time/residue: 0.5720 time to fit residues: 109.0498 Evaluate side-chains 73 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain A residue 699 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 598 ASN A 598 ASN ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13250 Z= 0.216 Angle : 0.470 4.620 17906 Z= 0.250 Chirality : 0.039 0.151 1974 Planarity : 0.003 0.039 2218 Dihedral : 11.080 93.069 2126 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.61 % Allowed : 4.16 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.22), residues: 1564 helix: 2.57 (0.18), residues: 858 sheet: 0.87 (0.44), residues: 140 loop : -0.79 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 933 HIS 0.005 0.001 HIS A 303 PHE 0.010 0.001 PHE A 984 TYR 0.012 0.001 TYR B 511 ARG 0.004 0.000 ARG B 644 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 1.860 Fit side-chains REVERT: B 420 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.6816 (pp) REVERT: B 699 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8316 (m-80) REVERT: A 420 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.6816 (pp) REVERT: A 699 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8328 (m-80) outliers start: 8 outliers final: 4 residues processed: 74 average time/residue: 0.4302 time to fit residues: 51.2376 Evaluate side-chains 62 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 792 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.0980 chunk 44 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13250 Z= 0.200 Angle : 0.430 5.005 17906 Z= 0.231 Chirality : 0.038 0.143 1974 Planarity : 0.003 0.033 2218 Dihedral : 10.452 88.200 2126 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.76 % Allowed : 3.86 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.22), residues: 1564 helix: 2.61 (0.18), residues: 856 sheet: 0.95 (0.44), residues: 140 loop : -0.78 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 933 HIS 0.006 0.001 HIS A 164 PHE 0.010 0.001 PHE A 984 TYR 0.009 0.001 TYR A 511 ARG 0.003 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 2.077 Fit side-chains REVERT: B 420 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7029 (pp) REVERT: B 699 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: A 420 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7033 (pp) REVERT: A 699 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.8306 (m-80) outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 0.4017 time to fit residues: 43.9298 Evaluate side-chains 67 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 989 CYS Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 989 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 827 HIS A 827 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13250 Z= 0.210 Angle : 0.423 5.095 17906 Z= 0.228 Chirality : 0.038 0.150 1974 Planarity : 0.003 0.029 2218 Dihedral : 10.184 87.756 2126 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.94 % Favored : 96.93 % Rotamer: Outliers : 0.76 % Allowed : 4.01 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.22), residues: 1564 helix: 2.65 (0.18), residues: 856 sheet: 0.90 (0.43), residues: 140 loop : -0.76 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 933 HIS 0.006 0.001 HIS B 164 PHE 0.011 0.001 PHE A 984 TYR 0.011 0.001 TYR A 511 ARG 0.003 0.000 ARG B 644 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 2.033 Fit side-chains REVERT: B 420 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7055 (pp) REVERT: B 699 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: A 420 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.6960 (pp) REVERT: A 699 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.8307 (m-80) outliers start: 10 outliers final: 6 residues processed: 67 average time/residue: 0.4965 time to fit residues: 55.5809 Evaluate side-chains 65 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 989 CYS Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 989 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13250 Z= 0.276 Angle : 0.458 5.440 17906 Z= 0.248 Chirality : 0.039 0.151 1974 Planarity : 0.003 0.028 2218 Dihedral : 10.534 89.544 2126 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 0.98 % Allowed : 4.39 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.22), residues: 1564 helix: 2.55 (0.18), residues: 854 sheet: 0.49 (0.43), residues: 140 loop : -0.64 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 693 HIS 0.006 0.001 HIS A 164 PHE 0.014 0.001 PHE A 984 TYR 0.011 0.001 TYR A 511 ARG 0.004 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 2.158 Fit side-chains REVERT: B 420 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7104 (pp) REVERT: B 699 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: B 765 MET cc_start: 0.8372 (tpt) cc_final: 0.8048 (tpt) REVERT: A 420 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7107 (pp) REVERT: A 699 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.8303 (m-80) outliers start: 13 outliers final: 8 residues processed: 68 average time/residue: 0.4153 time to fit residues: 46.8733 Evaluate side-chains 65 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 989 CYS Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 989 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13250 Z= 0.208 Angle : 0.419 5.937 17906 Z= 0.227 Chirality : 0.038 0.146 1974 Planarity : 0.003 0.027 2218 Dihedral : 10.338 90.431 2126 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.20 % Favored : 96.68 % Rotamer: Outliers : 0.91 % Allowed : 4.77 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.22), residues: 1564 helix: 2.63 (0.18), residues: 854 sheet: 0.35 (0.43), residues: 144 loop : -0.69 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 933 HIS 0.006 0.001 HIS A 164 PHE 0.010 0.001 PHE A 984 TYR 0.009 0.001 TYR A 511 ARG 0.002 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 2.015 Fit side-chains REVERT: B 420 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7134 (pp) REVERT: B 699 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: B 765 MET cc_start: 0.8399 (tpt) cc_final: 0.8093 (tpt) REVERT: A 420 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7138 (pp) REVERT: A 699 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.8245 (m-80) outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 0.4568 time to fit residues: 50.5370 Evaluate side-chains 62 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 989 CYS Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 989 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: