Starting phenix.real_space_refine on Fri Aug 9 09:45:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/08_2024/7stn_25434_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/08_2024/7stn_25434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/08_2024/7stn_25434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/08_2024/7stn_25434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/08_2024/7stn_25434_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/08_2024/7stn_25434_trim.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 8480 2.51 5 N 2062 2.21 5 O 2326 1.98 5 H 12256 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25188 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12400 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 24, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 12400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12400 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 24, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 231 Unusual residues: {'3PE': 5, 'BGI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {'3PE': 3, 'BGI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Time building chain proxies: 11.07, per 1000 atoms: 0.44 Number of scatterers: 25188 At special positions: 0 Unit cell: (135, 76.68, 120.96, 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 2326 8.00 N 2062 7.00 C 8480 6.00 H 12256 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: 18.04 Conformation dependent library (CDL) restraints added in 2.6 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 60.8% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.663A pdb=" N ARG A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.704A pdb=" N GLY A 245 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.872A 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: 3.588A pdb=" N TYR A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 343 removed outlier: 3.533A pdb=" N LEU A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.661A 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 380 Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.569A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 451 " --> pdb=" O TRP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 removed outlier: 3.537A pdb=" N VAL A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 removed outlier: 3.857A pdb=" N ASP A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 532 removed outlier: 3.531A pdb=" N TYR A 511 " --> pdb=" O ASN A 507 " (cutoff:3.500A) removed outlier: 4.747A 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: 3.574A pdb=" N LEU A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) removed outlier: 3.580A 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: 4.002A pdb=" N GLY A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.665A 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 603 removed outlier: 3.826A pdb=" N GLU A 603 " --> pdb=" O TYR A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 removed outlier: 3.937A pdb=" N CYS A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 609 " --> pdb=" O ARG A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 661 removed outlier: 4.138A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 667 removed outlier: 3.545A 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: 3.600A 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: 3.969A pdb=" N TYR A 754 " --> pdb=" O THR A 750 " (cutoff:3.500A) removed outlier: 3.813A 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: 4.092A pdb=" N ALA A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 831 removed outlier: 3.547A pdb=" N SER A 831 " --> pdb=" O HIS A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 853 removed outlier: 3.561A pdb=" N TYR A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) Proline residue: A 840 - end of helix removed outlier: 3.842A pdb=" N LEU A 846 " --> pdb=" O TYR A 842 " (cutoff:3.500A) removed outlier: 3.818A 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: 4.296A pdb=" N TYR A 921 " --> pdb=" O ASN A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 954 removed outlier: 3.987A pdb=" N ASN A 951 " --> pdb=" O GLY A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 1002 removed outlier: 3.887A pdb=" N ASN A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 155 removed outlier: 3.663A pdb=" N ARG B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.704A pdb=" N GLY B 245 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.872A 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: 3.588A pdb=" N TYR B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 343 removed outlier: 3.533A pdb=" N LEU B 326 " --> pdb=" O ASP B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 355 removed outlier: 3.661A 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 380 Processing helix chain 'B' and resid 439 through 451 removed outlier: 3.570A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 451 " --> pdb=" O TRP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 457 removed outlier: 3.537A pdb=" N VAL B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 485 removed outlier: 3.857A pdb=" N ASP B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 532 removed outlier: 3.531A pdb=" N TYR B 511 " --> pdb=" O ASN B 507 " (cutoff:3.500A) removed outlier: 4.747A 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: 3.575A pdb=" N LEU B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) removed outlier: 3.580A 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: 4.002A pdb=" N GLY B 565 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 3.665A 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 603 removed outlier: 3.826A pdb=" N GLU B 603 " --> pdb=" O TYR B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 613 removed outlier: 3.936A pdb=" N CYS B 608 " --> pdb=" O ASP B 604 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE B 609 " --> pdb=" O ARG B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 661 removed outlier: 4.139A pdb=" N ARG B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP B 647 " --> pdb=" O GLN B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 667 removed outlier: 3.544A 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: 3.600A 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: 3.969A pdb=" N TYR B 754 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 3.813A 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: 4.093A pdb=" N ALA B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 831 removed outlier: 3.546A pdb=" N SER B 831 " --> pdb=" O HIS B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 853 removed outlier: 3.562A pdb=" N TYR B 835 " --> pdb=" O SER B 831 " (cutoff:3.500A) Proline residue: B 840 - end of helix removed outlier: 3.842A pdb=" N LEU B 846 " --> pdb=" O TYR B 842 " (cutoff:3.500A) removed outlier: 3.818A 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: 4.296A pdb=" N TYR B 921 " --> pdb=" O ASN B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 954 removed outlier: 3.987A pdb=" N ASN B 951 " --> pdb=" O GLY B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 1002 removed outlier: 3.887A pdb=" N ASN B 961 " --> pdb=" O THR B 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.816A pdb=" N LYS B 874 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG A 391 " --> pdb=" O ALA B 873 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU B 875 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 252 removed outlier: 7.964A pdb=" N PHE A 279 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR A 405 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE A 357 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LEU A 431 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 359 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N CYS A 433 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 361 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS A 435 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N SER A 363 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE A 541 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY A 493 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ARG A 622 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA A 491 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N CYS A 624 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY A 493 " --> pdb=" O CYS A 624 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER A 626 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N ILE A 495 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ARG A 628 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N THR A 497 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLU A 630 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 409 through 413 removed outlier: 7.188A pdb=" N LYS A 419 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 240 removed outlier: 3.816A pdb=" N LYS A 874 " --> pdb=" O ASP A 882 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 248 through 252 removed outlier: 7.964A pdb=" N PHE B 279 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR B 405 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE B 357 " --> pdb=" O GLN B 429 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LEU B 431 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 359 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N CYS B 433 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE B 361 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS B 435 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N SER B 363 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE B 541 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY B 493 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ARG B 622 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA B 491 " --> pdb=" O ARG B 622 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N CYS B 624 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY B 493 " --> pdb=" O CYS B 624 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N SER B 626 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N ILE B 495 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ARG B 628 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N THR B 497 " --> pdb=" O ARG B 628 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLU B 630 " --> pdb=" O THR B 497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 409 through 413 removed outlier: 7.187A pdb=" N LYS B 419 " --> pdb=" O SER B 411 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 2085 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: 12.03 Time building geometry restraints manager: 19.18 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: 12232 1.03 - 1.23: 46 1.23 - 1.42: 5654 1.42 - 1.61: 7460 1.61 - 1.81: 106 Bond restraints: 25498 Sorted by residual: bond pdb=" C28 BGI B1202 " pdb=" N27 BGI B1202 " ideal model delta sigma weight residual 1.371 1.518 -0.147 2.00e-02 2.50e+03 5.44e+01 bond pdb=" C28 BGI A1202 " pdb=" N27 BGI A1202 " ideal model delta sigma weight residual 1.371 1.518 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C28 BGI A1202 " pdb=" N22 BGI A1202 " ideal model delta sigma weight residual 1.382 1.515 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" C28 BGI B1202 " pdb=" N22 BGI B1202 " ideal model delta sigma weight residual 1.382 1.514 -0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" C13 BGI B1202 " pdb=" N15 BGI B1202 " ideal model delta sigma weight residual 1.343 1.472 -0.129 2.00e-02 2.50e+03 4.19e+01 ... (remaining 25493 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.11: 392 107.11 - 113.83: 29184 113.83 - 120.54: 9336 120.54 - 127.26: 6611 127.26 - 133.98: 129 Bond angle restraints: 45652 Sorted by residual: angle pdb=" O12 3PE A1203 " pdb=" P 3PE A1203 " pdb=" O14 3PE A1203 " ideal model delta sigma weight residual 123.79 109.39 14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O12 3PE B1203 " pdb=" P 3PE B1203 " pdb=" O14 3PE B1203 " ideal model delta sigma weight residual 123.79 109.42 14.37 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O12 3PE A1206 " pdb=" P 3PE A1206 " pdb=" O14 3PE A1206 " ideal model delta sigma weight residual 123.79 109.44 14.35 3.00e+00 1.11e-01 2.29e+01 angle pdb=" O12 3PE A1204 " pdb=" P 3PE A1204 " pdb=" O14 3PE A1204 " ideal model delta sigma weight residual 123.79 109.47 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 3PE B1204 " pdb=" P 3PE B1204 " pdb=" O14 3PE B1204 " ideal model delta sigma weight residual 123.79 109.48 14.31 3.00e+00 1.11e-01 2.28e+01 ... (remaining 45647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 11595 17.84 - 35.69: 448 35.69 - 53.53: 195 53.53 - 71.38: 50 71.38 - 89.22: 14 Dihedral angle restraints: 12302 sinusoidal: 6540 harmonic: 5762 Sorted by residual: dihedral pdb=" N TYR B 699 " pdb=" CA TYR B 699 " pdb=" CB TYR B 699 " pdb=" CG TYR B 699 " ideal model delta sinusoidal sigma weight residual -60.00 -114.31 54.31 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" N TYR A 699 " pdb=" CA TYR A 699 " pdb=" CB TYR A 699 " pdb=" CG TYR A 699 " ideal model delta sinusoidal sigma weight residual -60.00 -114.28 54.28 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CB ARG A 645 " pdb=" CG ARG A 645 " pdb=" CD ARG A 645 " pdb=" NE ARG A 645 " ideal model delta sinusoidal sigma weight residual 60.00 111.47 -51.47 3 1.50e+01 4.44e-03 9.02e+00 ... (remaining 12299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1896 0.099 - 0.199: 74 0.199 - 0.298: 2 0.298 - 0.398: 0 0.398 - 0.497: 2 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C19 BGI A1202 " pdb=" C18 BGI A1202 " pdb=" C20 BGI A1202 " pdb=" O30 BGI A1202 " both_signs ideal model delta sigma weight residual False 2.48 2.97 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" C19 BGI B1202 " pdb=" C18 BGI B1202 " pdb=" C20 BGI B1202 " pdb=" O30 BGI B1202 " both_signs ideal model delta sigma weight residual False 2.48 2.97 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" C18 BGI B1202 " pdb=" C17 BGI B1202 " pdb=" C19 BGI B1202 " pdb=" O31 BGI B1202 " both_signs ideal model delta sigma weight residual False 2.72 2.92 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1971 not shown) Planarity restraints: 3738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 945 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" N GLU B 946 " -0.033 2.00e-02 2.50e+03 pdb=" CA GLU B 946 " 0.009 2.00e-02 2.50e+03 pdb=" H GLU B 946 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 945 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" N GLU A 946 " -0.033 2.00e-02 2.50e+03 pdb=" CA GLU A 946 " 0.009 2.00e-02 2.50e+03 pdb=" H GLU A 946 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 943 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" N VAL A 944 " -0.030 2.00e-02 2.50e+03 pdb=" CA VAL A 944 " 0.008 2.00e-02 2.50e+03 pdb=" H VAL A 944 " 0.013 2.00e-02 2.50e+03 ... (remaining 3735 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1055 2.21 - 2.80: 50880 2.80 - 3.40: 67180 3.40 - 4.00: 87425 4.00 - 4.60: 139624 Nonbonded interactions: 346164 Sorted by model distance: nonbonded pdb=" OE1 GLU A 341 " pdb=" HG SER A 353 " model vdw 1.608 2.450 nonbonded pdb=" OE1 GLU B 341 " pdb=" HG SER B 353 " model vdw 1.608 2.450 nonbonded pdb=" O VAL B 665 " pdb=" HG SER B 668 " model vdw 1.670 2.450 nonbonded pdb=" O VAL A 665 " pdb=" HG SER A 668 " model vdw 1.671 2.450 nonbonded pdb=" OE1 GLN A 834 " pdb=" H GLN A 834 " model vdw 1.681 2.450 ... (remaining 346159 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 1204)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.010 Normalize map: mean=0, sd=1: 0.480 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: 0.380 Extract box with map and model: 0.870 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 82.680 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 : 0.006 0.147 13242 Z= 0.420 Angle : 0.776 14.398 17896 Z= 0.323 Chirality : 0.042 0.497 1974 Planarity : 0.002 0.030 2214 Dihedral : 11.717 89.221 4922 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.15 % Allowed : 1.67 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.22), residues: 1564 helix: 3.01 (0.17), residues: 828 sheet: 1.12 (0.45), residues: 140 loop : -0.60 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 933 HIS 0.002 0.000 HIS A 679 PHE 0.008 0.001 PHE B 984 TYR 0.007 0.001 TYR B 731 ARG 0.002 0.000 ARG B 926 *********************** 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 142 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 4.056 Fit side-chains REVERT: A 699 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: B 699 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7592 (m-80) outliers start: 2 outliers final: 0 residues processed: 142 average time/residue: 0.6483 time to fit residues: 128.6427 Evaluate side-chains 63 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B 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: 1.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 40.0000 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN B 582 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13242 Z= 0.310 Angle : 0.491 5.263 17896 Z= 0.266 Chirality : 0.040 0.155 1974 Planarity : 0.003 0.038 2214 Dihedral : 11.368 91.840 2110 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.83 % Allowed : 4.77 % Favored : 94.39 % 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: 2.08 (0.22), residues: 1564 helix: 2.63 (0.17), residues: 868 sheet: 1.01 (0.45), residues: 140 loop : -0.61 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 933 HIS 0.002 0.001 HIS B 303 PHE 0.014 0.001 PHE B 984 TYR 0.008 0.001 TYR B 842 ARG 0.003 0.001 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: 11 poor density : 63 time to evaluate : 2.018 Fit side-chains REVERT: A 147 ASP cc_start: 0.6348 (OUTLIER) cc_final: 0.6031 (p0) REVERT: A 699 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: A 800 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: B 699 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: B 800 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7368 (tt0) outliers start: 11 outliers final: 4 residues processed: 72 average time/residue: 0.5445 time to fit residues: 58.5448 Evaluate side-chains 67 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 598 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 13242 Z= 0.238 Angle : 0.442 5.006 17896 Z= 0.238 Chirality : 0.038 0.149 1974 Planarity : 0.003 0.034 2214 Dihedral : 10.705 90.919 2110 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.68 % Allowed : 5.38 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.22), residues: 1564 helix: 2.71 (0.18), residues: 852 sheet: 1.13 (0.45), residues: 140 loop : -0.56 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 933 HIS 0.002 0.001 HIS B 679 PHE 0.012 0.001 PHE B 984 TYR 0.008 0.001 TYR B 842 ARG 0.007 0.000 ARG A 281 *********************** 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 62 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 1.859 Fit side-chains revert: symmetry clash REVERT: A 699 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: B 699 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7771 (m-80) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.6639 time to fit residues: 58.3602 Evaluate side-chains 61 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU 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: 6.9990 chunk 74 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A 797 GLN B 429 GLN B 797 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 13242 Z= 0.442 Angle : 0.557 5.435 17896 Z= 0.308 Chirality : 0.042 0.157 1974 Planarity : 0.004 0.040 2214 Dihedral : 11.888 89.753 2110 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.98 % Allowed : 5.91 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1564 helix: 2.13 (0.17), residues: 848 sheet: 0.61 (0.44), residues: 130 loop : -0.76 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 693 HIS 0.003 0.001 HIS B 679 PHE 0.022 0.002 PHE B 541 TYR 0.014 0.002 TYR B 404 ARG 0.005 0.001 ARG A 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: 13 poor density : 56 time to evaluate : 2.078 Fit side-chains REVERT: A 699 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: A 800 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7538 (tt0) REVERT: B 699 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: B 800 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7536 (tt0) outliers start: 13 outliers final: 9 residues processed: 65 average time/residue: 0.5609 time to fit residues: 54.2399 Evaluate side-chains 65 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13242 Z= 0.279 Angle : 0.460 5.099 17896 Z= 0.254 Chirality : 0.039 0.139 1974 Planarity : 0.003 0.034 2214 Dihedral : 11.186 91.002 2110 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.91 % Allowed : 6.52 % Favored : 92.58 % 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: 1.63 (0.21), residues: 1564 helix: 2.32 (0.17), residues: 848 sheet: 0.54 (0.44), residues: 130 loop : -0.68 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 933 HIS 0.002 0.001 HIS B 679 PHE 0.014 0.001 PHE A 984 TYR 0.009 0.001 TYR B 684 ARG 0.002 0.000 ARG A 372 *********************** 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 65 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 1.878 Fit side-chains REVERT: A 699 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: A 800 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: B 699 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: B 800 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7519 (tt0) outliers start: 12 outliers final: 7 residues processed: 60 average time/residue: 0.6707 time to fit residues: 59.7695 Evaluate side-chains 64 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -build -allalt -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: