Starting phenix.real_space_refine on Mon Oct 14 18:26:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3q_17392/10_2024/8p3q_17392.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3q_17392/10_2024/8p3q_17392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3q_17392/10_2024/8p3q_17392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3q_17392/10_2024/8p3q_17392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3q_17392/10_2024/8p3q_17392.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3q_17392/10_2024/8p3q_17392.cif" } resolution = 2.95 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 125 5.16 5 C 11851 2.51 5 N 2840 2.21 5 O 3226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 18047 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3059 Classifications: {'peptide': 399} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 386} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3037 Classifications: {'peptide': 398} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 385} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3024 Classifications: {'peptide': 396} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 383} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3025 Classifications: {'peptide': 397} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 13} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 384} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1364 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1373 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1369 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 82 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'PLM': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 11.37, per 1000 atoms: 0.63 Number of scatterers: 18047 At special positions: 0 Unit cell: (121.422, 119.977, 135.877, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 125 16.00 P 5 15.00 O 3226 8.00 N 2840 7.00 C 11851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.04 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.02 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.04 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.02 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.04 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.02 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.85 Conformation dependent library (CDL) restraints added in 2.3 seconds 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4166 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 27 sheets defined 61.0% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.741A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 575 through 585 Processing helix chain 'A' and resid 595 through 629 Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.526A pdb=" N GLY A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 714 Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 767 Processing helix chain 'A' and resid 788 through 820 removed outlier: 3.752A pdb=" N VAL A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLY A 794 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.702A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 624 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 677 removed outlier: 3.564A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 822 removed outlier: 3.664A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 822 " --> pdb=" O SER B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 removed outlier: 3.738A pdb=" N TRP C 551 " --> pdb=" O PRO C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 624 Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 677 removed outlier: 3.927A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 705 through 714 removed outlier: 3.562A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 757 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 820 removed outlier: 3.733A pdb=" N VAL C 792 " --> pdb=" O SER C 788 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLY C 794 " --> pdb=" O SER C 790 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 423 through 436 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.611A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 545 removed outlier: 3.512A pdb=" N TRP D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.646A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.566A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 823 removed outlier: 3.719A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 30 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 133 through 161 removed outlier: 3.727A pdb=" N SER E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 210 removed outlier: 3.705A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 93 through 104 Processing helix chain 'F' and resid 105 through 127 removed outlier: 4.102A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 160 Processing helix chain 'F' and resid 177 through 209 Processing helix chain 'G' and resid 7 through 30 Processing helix chain 'G' and resid 93 through 104 Processing helix chain 'G' and resid 105 through 127 removed outlier: 3.745A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 161 Processing helix chain 'G' and resid 177 through 210 Processing helix chain 'H' and resid 6 through 30 removed outlier: 3.521A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 105 through 124 Processing helix chain 'H' and resid 132 through 161 removed outlier: 4.137A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 210 removed outlier: 3.861A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 480 through 481 removed outlier: 4.234A pdb=" N GLY A 731 " --> pdb=" O ILE A 481 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA5, first strand: chain 'A' and resid 502 through 505 removed outlier: 3.725A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 646 through 648 removed outlier: 5.745A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 394 through 399 Processing sheet with id=AA8, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB1, first strand: chain 'B' and resid 497 through 498 Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 5.994A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 394 through 399 Processing sheet with id=AB4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'C' and resid 489 through 498 removed outlier: 4.836A pdb=" N ILE C 734 " --> pdb=" O SER C 492 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C 732 " --> pdb=" O PRO C 494 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N MET C 496 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS C 730 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 502 through 505 Processing sheet with id=AB7, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.340A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 440 through 444 Processing sheet with id=AB9, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC1, first strand: chain 'D' and resid 489 through 498 removed outlier: 6.969A pdb=" N SER D 492 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR D 736 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE D 734 " --> pdb=" O PRO D 494 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 5.669A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR D 702 " --> pdb=" O MET D 503 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET D 503 " --> pdb=" O TYR D 702 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AC4, first strand: chain 'F' and resid 57 through 59 Processing sheet with id=AC5, first strand: chain 'F' and resid 65 through 67 Processing sheet with id=AC6, first strand: chain 'G' and resid 57 through 61 Processing sheet with id=AC7, first strand: chain 'G' and resid 65 through 67 Processing sheet with id=AC8, first strand: chain 'H' and resid 57 through 59 Processing sheet with id=AC9, first strand: chain 'H' and resid 65 through 66 1122 hydrogen bonds defined for protein. 3240 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: 5.82 Time building geometry restraints manager: 5.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2800 1.32 - 1.45: 5145 1.45 - 1.58: 10263 1.58 - 1.71: 10 1.71 - 1.84: 202 Bond restraints: 18420 Sorted by residual: bond pdb=" C VAL B 484 " pdb=" N ARG B 485 " ideal model delta sigma weight residual 1.334 1.410 -0.075 1.33e-02 5.65e+03 3.22e+01 bond pdb=" C ALA C 691 " pdb=" N ARG C 692 " ideal model delta sigma weight residual 1.335 1.392 -0.057 1.31e-02 5.83e+03 1.90e+01 bond pdb=" CA SER C 537 " pdb=" CB SER C 537 " ideal model delta sigma weight residual 1.528 1.464 0.065 1.56e-02 4.11e+03 1.74e+01 bond pdb=" C LEU A 742 " pdb=" N ARG A 743 " ideal model delta sigma weight residual 1.335 1.387 -0.053 1.27e-02 6.20e+03 1.71e+01 bond pdb=" CA SER D 537 " pdb=" CB SER D 537 " ideal model delta sigma weight residual 1.529 1.466 0.063 1.55e-02 4.16e+03 1.63e+01 ... (remaining 18415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 21357 1.92 - 3.84: 3114 3.84 - 5.76: 287 5.76 - 7.68: 44 7.68 - 9.60: 7 Bond angle restraints: 24809 Sorted by residual: angle pdb=" O VAL B 484 " pdb=" C VAL B 484 " pdb=" N ARG B 485 " ideal model delta sigma weight residual 121.87 131.47 -9.60 1.01e+00 9.80e-01 9.04e+01 angle pdb=" CA ALA B 477 " pdb=" C ALA B 477 " pdb=" N PRO B 478 " ideal model delta sigma weight residual 117.68 122.31 -4.63 7.10e-01 1.98e+00 4.26e+01 angle pdb=" O MET D 674 " pdb=" C MET D 674 " pdb=" N ARG D 675 " ideal model delta sigma weight residual 122.12 128.81 -6.69 1.06e+00 8.90e-01 3.99e+01 angle pdb=" O ALA D 452 " pdb=" C ALA D 452 " pdb=" N ARG D 453 " ideal model delta sigma weight residual 123.41 116.30 7.11 1.17e+00 7.31e-01 3.70e+01 angle pdb=" CA GLU D 678 " pdb=" C GLU D 678 " pdb=" O GLU D 678 " ideal model delta sigma weight residual 119.99 114.87 5.12 8.70e-01 1.32e+00 3.46e+01 ... (remaining 24804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.57: 10106 31.57 - 63.15: 621 63.15 - 94.72: 44 94.72 - 126.29: 5 126.29 - 157.87: 2 Dihedral angle restraints: 10778 sinusoidal: 4237 harmonic: 6541 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual 93.00 4.92 88.08 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 12.31 80.69 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual -86.00 -13.66 -72.34 1 1.00e+01 1.00e-02 6.69e+01 ... (remaining 10775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1670 0.069 - 0.137: 891 0.137 - 0.206: 181 0.206 - 0.275: 19 0.275 - 0.344: 7 Chirality restraints: 2768 Sorted by residual: chirality pdb=" CB VAL B 543 " pdb=" CA VAL B 543 " pdb=" CG1 VAL B 543 " pdb=" CG2 VAL B 543 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CG LEU A 498 " pdb=" CB LEU A 498 " pdb=" CD1 LEU A 498 " pdb=" CD2 LEU A 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CG LEU B 498 " pdb=" CB LEU B 498 " pdb=" CD1 LEU B 498 " pdb=" CD2 LEU B 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 2765 not shown) Planarity restraints: 3018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV G1103 " 0.026 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C29 POV G1103 " -0.064 2.00e-02 2.50e+03 pdb="C210 POV G1103 " 0.064 2.00e-02 2.50e+03 pdb="C211 POV G1103 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 541 " 0.028 2.00e-02 2.50e+03 3.15e-02 1.74e+01 pdb=" CG PHE B 541 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE B 541 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 541 " -0.061 2.00e-02 2.50e+03 pdb=" CE1 PHE B 541 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE B 541 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE B 541 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 485 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ARG B 485 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG B 485 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU B 486 " -0.022 2.00e-02 2.50e+03 ... (remaining 3015 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6014 2.83 - 3.35: 18383 3.35 - 3.86: 32697 3.86 - 4.38: 38989 4.38 - 4.90: 61010 Nonbonded interactions: 157093 Sorted by model distance: nonbonded pdb=" O ARG A 453 " pdb=" C ASP A 454 " model vdw 2.310 3.270 nonbonded pdb=" O LEU E 63 " pdb=" NH2 ARG E 102 " model vdw 2.363 3.120 nonbonded pdb=" O ARG G 6 " pdb=" N VAL G 8 " model vdw 2.365 3.120 nonbonded pdb=" O SER E 104 " pdb=" OG SER E 104 " model vdw 2.433 3.040 nonbonded pdb=" O ARG E 131 " pdb=" N ASN E 133 " model vdw 2.438 3.120 ... (remaining 157088 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 393 through 593 or (resid 594 and (name N or name CA or na \ me C or name O or name CB )) or resid 595 through 625 or resid 635 through 812 o \ r (resid 813 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 14 through 818 or (resid 819 through 823 and (name N or name CA or name C or nam \ e O or name CB )))) selection = (chain 'B' and (resid 393 through 510 or (resid 511 and (name N or name CA or na \ me C or name O or name CB )) or resid 512 through 551 or (resid 569 and (name N \ or name CA or name C or name O or name CB )) or resid 570 through 593 or (resid \ 594 and (name N or name CA or name C or name O or name CB )) or resid 595 throug \ h 625 or resid 635 through 773 or resid 785 through 823)) selection = (chain 'C' and (resid 393 through 625 or resid 635 through 812 or (resid 813 and \ (name N or name CA or name C or name O or name CB )) or resid 814 through 818 o \ r (resid 819 through 823 and (name N or name CA or name C or name O or name CB ) \ ))) selection = (chain 'D' and (resid 393 through 551 or (resid 569 and (name N or name CA or na \ me C or name O or name CB )) or resid 570 through 593 or (resid 594 and (name N \ or name CA or name C or name O or name CB )) or resid 595 through 625 or resid 6 \ 35 through 773 or resid 785 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 84 or resid 93 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 55 through 84 or resid 93 through 21 \ 0)) selection = (chain 'G' and (resid 5 through 84 or resid 93 through 206 or (resid 207 and (na \ me N or name CA or name C or name O or name CB )) or resid 208 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 206 or (resid 207 and (na \ me N or name CA or name C or name O or name CB )) or resid 208 through 210)) } 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: 0.720 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 41.600 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.070 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:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.010 0.075 18420 Z= 0.626 Angle : 1.369 9.604 24809 Z= 0.947 Chirality : 0.080 0.344 2768 Planarity : 0.009 0.076 3018 Dihedral : 18.610 157.867 6576 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.98 % Allowed : 5.86 % Favored : 93.15 % Rotamer: Outliers : 9.79 % Allowed : 8.42 % Favored : 81.79 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 21.43 % 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: -1.51 (0.16), residues: 2235 helix: 0.03 (0.14), residues: 1302 sheet: -2.14 (0.38), residues: 126 loop : -2.49 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.007 TRP A 606 HIS 0.018 0.005 HIS D 435 PHE 0.061 0.007 PHE B 541 TYR 0.038 0.006 TYR D 549 ARG 0.041 0.004 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 325 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7294 (mmt) REVERT: A 481 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8605 (OUTLIER) REVERT: A 503 MET cc_start: 0.7829 (ttm) cc_final: 0.7314 (ptm) REVERT: A 506 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8180 (ttmm) REVERT: A 713 GLU cc_start: 0.9325 (tt0) cc_final: 0.8923 (tp30) REVERT: A 721 MET cc_start: 0.9029 (ttt) cc_final: 0.8661 (tpp) REVERT: B 543 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8733 (m) REVERT: B 586 ARG cc_start: 0.9324 (mmm-85) cc_final: 0.8873 (mmm160) REVERT: B 770 LYS cc_start: 0.4185 (OUTLIER) cc_final: 0.3138 (mmmt) REVERT: C 407 MET cc_start: 0.2826 (OUTLIER) cc_final: 0.1439 (ptt) REVERT: C 408 MET cc_start: 0.1356 (mmm) cc_final: 0.0498 (pmm) REVERT: C 414 MET cc_start: 0.5990 (OUTLIER) cc_final: 0.4498 (ptt) REVERT: C 633 ILE cc_start: 0.5540 (OUTLIER) cc_final: 0.5308 (mm) REVERT: C 647 TYR cc_start: 0.3256 (p90) cc_final: 0.2299 (p90) REVERT: C 666 VAL cc_start: 0.4182 (OUTLIER) cc_final: 0.3961 (p) REVERT: C 714 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7927 (mp10) REVERT: C 819 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8450 (ttt-90) REVERT: E 57 VAL cc_start: 0.9292 (OUTLIER) cc_final: 0.9025 (p) REVERT: E 69 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8944 (pt) REVERT: E 76 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9151 (mm) REVERT: E 95 GLU cc_start: 0.9414 (mm-30) cc_final: 0.8931 (tp30) REVERT: F 9 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8951 (mt0) REVERT: F 10 MET cc_start: 0.9339 (tpp) cc_final: 0.8998 (mmm) REVERT: F 24 MET cc_start: 0.8564 (tpt) cc_final: 0.7937 (tpp) REVERT: F 69 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8931 (pt) REVERT: F 81 ASP cc_start: 0.9109 (t0) cc_final: 0.8649 (t0) REVERT: F 95 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: F 99 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8646 (mtm180) REVERT: G 37 ARG cc_start: 0.8543 (mtp85) cc_final: 0.8143 (mmm-85) REVERT: G 41 LYS cc_start: 0.8533 (tptp) cc_final: 0.8130 (pptt) REVERT: G 131 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8490 (mmm160) REVERT: G 207 GLN cc_start: 0.9353 (mm-40) cc_final: 0.9132 (pt0) REVERT: H 5 ASP cc_start: 0.6294 (m-30) cc_final: 0.5906 (m-30) REVERT: H 9 GLN cc_start: 0.8586 (mt0) cc_final: 0.8324 (mp-120) REVERT: H 41 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8279 (tptp) REVERT: H 78 LYS cc_start: 0.9146 (ptmt) cc_final: 0.8436 (pttm) REVERT: H 81 ASP cc_start: 0.9296 (t70) cc_final: 0.9060 (t70) REVERT: H 207 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8519 (mm110) outliers start: 178 outliers final: 41 residues processed: 468 average time/residue: 1.4863 time to fit residues: 768.7457 Evaluate side-chains 248 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 190 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 817 LYS Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 819 ARG Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 506 LYS Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 692 ARG Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 96 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 90 optimal weight: 0.0270 chunk 175 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN A 619 ASN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS C 587 GLN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 ASN D 587 GLN D 619 ASN D 756 GLN E 160 ASN E 199 HIS F 60 HIS F 132 HIS F 160 ASN F 205 HIS G 160 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18420 Z= 0.212 Angle : 0.641 10.305 24809 Z= 0.335 Chirality : 0.042 0.190 2768 Planarity : 0.004 0.042 3018 Dihedral : 13.423 115.448 2932 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.18 % Favored : 96.55 % Rotamer: Outliers : 4.84 % Allowed : 18.21 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2235 helix: 1.77 (0.15), residues: 1324 sheet: -2.36 (0.38), residues: 113 loop : -1.80 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 766 HIS 0.005 0.001 HIS D 435 PHE 0.019 0.002 PHE H 127 TYR 0.017 0.002 TYR D 711 ARG 0.007 0.001 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 243 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7904 (mmm) cc_final: 0.7511 (mmt) REVERT: A 503 MET cc_start: 0.7826 (ttm) cc_final: 0.7252 (ptm) REVERT: A 759 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6010 (mt) REVERT: B 407 MET cc_start: 0.7682 (ppp) cc_final: 0.7480 (ppp) REVERT: B 408 MET cc_start: 0.6502 (mmm) cc_final: 0.6109 (mpp) REVERT: B 586 ARG cc_start: 0.9194 (mmm-85) cc_final: 0.8886 (mmm160) REVERT: B 692 ARG cc_start: 0.9104 (mmm-85) cc_final: 0.8876 (tpm170) REVERT: B 770 LYS cc_start: 0.4211 (OUTLIER) cc_final: 0.3220 (mmmt) REVERT: C 408 MET cc_start: 0.1979 (mmm) cc_final: 0.1680 (mpt) REVERT: C 414 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.5750 (ptt) REVERT: C 463 MET cc_start: 0.2362 (mtm) cc_final: 0.1488 (ptp) REVERT: C 496 MET cc_start: 0.3610 (mtt) cc_final: 0.2422 (tpt) REVERT: C 674 MET cc_start: 0.3779 (mtt) cc_final: 0.3413 (mtp) REVERT: C 714 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7933 (mp10) REVERT: D 414 MET cc_start: 0.5234 (OUTLIER) cc_final: 0.4391 (pp-130) REVERT: D 703 LEU cc_start: 0.8528 (mt) cc_final: 0.8180 (tp) REVERT: D 705 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8898 (mm-30) REVERT: E 37 ARG cc_start: 0.9130 (ttm-80) cc_final: 0.8802 (ttm-80) REVERT: E 57 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.9129 (t) REVERT: E 95 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9014 (tp30) REVERT: E 102 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8570 (tpt90) REVERT: F 6 ARG cc_start: 0.8682 (tpt90) cc_final: 0.8345 (tpt90) REVERT: F 69 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8005 (pt) REVERT: F 81 ASP cc_start: 0.9218 (t0) cc_final: 0.8800 (t0) REVERT: G 24 MET cc_start: 0.8940 (tpt) cc_final: 0.8738 (tpt) REVERT: G 204 ARG cc_start: 0.9005 (ttm-80) cc_final: 0.8763 (ttm-80) REVERT: G 207 GLN cc_start: 0.9349 (mm-40) cc_final: 0.9079 (pt0) REVERT: G 208 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9004 (mp) REVERT: H 5 ASP cc_start: 0.5973 (m-30) cc_final: 0.5222 (m-30) REVERT: H 6 ARG cc_start: 0.8031 (tmm160) cc_final: 0.7758 (tmm160) REVERT: H 9 GLN cc_start: 0.8474 (mt0) cc_final: 0.7962 (mp10) REVERT: H 78 LYS cc_start: 0.9101 (ptmt) cc_final: 0.8418 (pttm) REVERT: H 81 ASP cc_start: 0.9301 (t70) cc_final: 0.9064 (t0) outliers start: 88 outliers final: 23 residues processed: 311 average time/residue: 1.2888 time to fit residues: 449.6331 Evaluate side-chains 212 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 73 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN C 709 ASN D 569 ASN D 619 ASN D 791 ASN E 132 HIS F 9 GLN G 133 ASN G 160 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18420 Z= 0.312 Angle : 0.620 10.274 24809 Z= 0.323 Chirality : 0.042 0.212 2768 Planarity : 0.004 0.047 3018 Dihedral : 11.798 89.118 2838 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.67 % Favored : 96.06 % Rotamer: Outliers : 4.95 % Allowed : 19.42 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2235 helix: 2.08 (0.15), residues: 1334 sheet: -2.79 (0.34), residues: 126 loop : -1.65 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 766 HIS 0.005 0.001 HIS G 60 PHE 0.021 0.002 PHE F 83 TYR 0.021 0.002 TYR C 647 ARG 0.008 0.001 ARG C 675 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 180 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7727 (mpp) cc_final: 0.7403 (mpp) REVERT: A 408 MET cc_start: 0.7967 (mmm) cc_final: 0.7681 (mmt) REVERT: A 503 MET cc_start: 0.7697 (ttm) cc_final: 0.7105 (ptm) REVERT: A 629 MET cc_start: 0.9069 (ptm) cc_final: 0.8844 (ptp) REVERT: A 759 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.5960 (mt) REVERT: B 408 MET cc_start: 0.6487 (mmm) cc_final: 0.6124 (mpp) REVERT: B 586 ARG cc_start: 0.9340 (mmm-85) cc_final: 0.9020 (mmm160) REVERT: C 414 MET cc_start: 0.7363 (mtm) cc_final: 0.5788 (ptt) REVERT: C 496 MET cc_start: 0.4236 (mtt) cc_final: 0.3441 (tpt) REVERT: C 714 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7598 (mp10) REVERT: D 496 MET cc_start: 0.3218 (OUTLIER) cc_final: 0.2969 (ttm) REVERT: D 590 ASP cc_start: 0.8730 (m-30) cc_final: 0.8420 (t0) REVERT: E 5 ASP cc_start: 0.6001 (OUTLIER) cc_final: 0.5593 (p0) REVERT: E 37 ARG cc_start: 0.9235 (ttm-80) cc_final: 0.8882 (ttm-80) REVERT: E 57 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8963 (t) REVERT: E 95 GLU cc_start: 0.9373 (mm-30) cc_final: 0.9118 (tm-30) REVERT: E 102 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8293 (tpt90) REVERT: E 174 TYR cc_start: 0.8786 (p90) cc_final: 0.8563 (p90) REVERT: F 10 MET cc_start: 0.9247 (mmm) cc_final: 0.9032 (mmm) REVERT: F 69 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8571 (pt) REVERT: F 81 ASP cc_start: 0.9180 (t0) cc_final: 0.8813 (t0) REVERT: F 95 GLU cc_start: 0.9015 (tp30) cc_final: 0.8688 (tp30) REVERT: F 191 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8667 (mm-30) REVERT: G 207 GLN cc_start: 0.9290 (mm-40) cc_final: 0.9036 (pt0) REVERT: H 5 ASP cc_start: 0.5745 (m-30) cc_final: 0.5179 (m-30) REVERT: H 9 GLN cc_start: 0.8696 (mt0) cc_final: 0.8182 (mp10) REVERT: H 31 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: H 78 LYS cc_start: 0.9027 (ptmt) cc_final: 0.8522 (ptpt) REVERT: H 81 ASP cc_start: 0.9253 (t0) cc_final: 0.9016 (t0) outliers start: 90 outliers final: 50 residues processed: 252 average time/residue: 1.3377 time to fit residues: 378.1026 Evaluate side-chains 213 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 156 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain C residue 670 MET Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 60 HIS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 105 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 204 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 569 ASN D 619 ASN F 160 ASN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN H 149 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18420 Z= 0.190 Angle : 0.572 9.631 24809 Z= 0.295 Chirality : 0.040 0.175 2768 Planarity : 0.004 0.047 3018 Dihedral : 10.894 88.528 2829 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.09 % Favored : 96.69 % Rotamer: Outliers : 4.57 % Allowed : 20.63 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.24 (0.19), residues: 2235 helix: 2.44 (0.15), residues: 1335 sheet: -2.71 (0.35), residues: 133 loop : -1.56 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 766 HIS 0.004 0.001 HIS F 205 PHE 0.016 0.001 PHE F 83 TYR 0.014 0.001 TYR C 647 ARG 0.011 0.001 ARG B 743 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 191 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7318 (mpp) REVERT: A 503 MET cc_start: 0.7698 (ttm) cc_final: 0.7160 (ptm) REVERT: A 759 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.5957 (mt) REVERT: B 408 MET cc_start: 0.6385 (mmm) cc_final: 0.6128 (mpp) REVERT: B 586 ARG cc_start: 0.9136 (mmm-85) cc_final: 0.8762 (mmm160) REVERT: C 414 MET cc_start: 0.7424 (mtm) cc_final: 0.5952 (ptt) REVERT: C 463 MET cc_start: 0.3063 (mpp) cc_final: 0.2570 (tpp) REVERT: C 496 MET cc_start: 0.3887 (mtt) cc_final: 0.3381 (tpt) REVERT: C 586 ARG cc_start: 0.9081 (ttm110) cc_final: 0.8836 (ttm110) REVERT: C 670 MET cc_start: 0.6851 (mtp) cc_final: 0.6438 (ptp) REVERT: C 714 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7739 (mp10) REVERT: C 819 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8417 (ttt-90) REVERT: D 407 MET cc_start: 0.6880 (mpp) cc_final: 0.6373 (mpm) REVERT: D 408 MET cc_start: 0.4898 (tpp) cc_final: 0.4620 (tpp) REVERT: D 414 MET cc_start: 0.5729 (OUTLIER) cc_final: 0.4873 (pmm) REVERT: D 496 MET cc_start: 0.3260 (ttm) cc_final: 0.2480 (tmm) REVERT: D 736 THR cc_start: 0.4759 (OUTLIER) cc_final: 0.4233 (t) REVERT: E 5 ASP cc_start: 0.5800 (OUTLIER) cc_final: 0.5278 (p0) REVERT: E 95 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9100 (tm-30) REVERT: E 102 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8368 (tpt90) REVERT: E 174 TYR cc_start: 0.8711 (p90) cc_final: 0.8478 (p90) REVERT: F 10 MET cc_start: 0.9246 (mmm) cc_final: 0.9022 (mmm) REVERT: F 81 ASP cc_start: 0.9160 (t0) cc_final: 0.8794 (t0) REVERT: F 95 GLU cc_start: 0.8943 (tp30) cc_final: 0.8646 (tp30) REVERT: G 60 HIS cc_start: 0.8837 (OUTLIER) cc_final: 0.8418 (p90) REVERT: H 5 ASP cc_start: 0.5945 (m-30) cc_final: 0.5438 (m-30) REVERT: H 9 GLN cc_start: 0.8614 (mt0) cc_final: 0.8051 (mp10) REVERT: H 78 LYS cc_start: 0.9004 (ptmt) cc_final: 0.8659 (pttm) REVERT: H 203 ASP cc_start: 0.9444 (t0) cc_final: 0.9210 (t0) outliers start: 83 outliers final: 40 residues processed: 258 average time/residue: 1.3247 time to fit residues: 385.4209 Evaluate side-chains 215 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 819 ARG Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 89 optimal weight: 30.0000 chunk 184 optimal weight: 0.9980 chunk 149 optimal weight: 0.2980 chunk 0 optimal weight: 50.0000 chunk 110 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 569 ASN D 619 ASN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN G 205 HIS ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 18420 Z= 0.249 Angle : 0.600 11.445 24809 Z= 0.308 Chirality : 0.041 0.230 2768 Planarity : 0.004 0.047 3018 Dihedral : 10.536 88.205 2821 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.27 % Favored : 96.51 % Rotamer: Outliers : 4.68 % Allowed : 20.57 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.38 (0.19), residues: 2235 helix: 2.54 (0.14), residues: 1332 sheet: -2.69 (0.35), residues: 133 loop : -1.43 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 766 HIS 0.008 0.001 HIS D 435 PHE 0.020 0.001 PHE D 623 TYR 0.022 0.001 TYR C 711 ARG 0.007 0.001 ARG G 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 180 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8039 (mmt) cc_final: 0.7784 (mmp) REVERT: A 503 MET cc_start: 0.7653 (ttm) cc_final: 0.7384 (ptm) REVERT: A 756 GLN cc_start: 0.5834 (OUTLIER) cc_final: 0.5130 (pp30) REVERT: A 759 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6333 (mt) REVERT: B 586 ARG cc_start: 0.9217 (mmm-85) cc_final: 0.8784 (mmm160) REVERT: C 414 MET cc_start: 0.7511 (mtm) cc_final: 0.6137 (ptt) REVERT: C 463 MET cc_start: 0.3101 (mpp) cc_final: 0.2479 (tpp) REVERT: C 496 MET cc_start: 0.4391 (mtt) cc_final: 0.3169 (tpt) REVERT: C 674 MET cc_start: 0.3600 (mtt) cc_final: 0.3135 (mtp) REVERT: C 714 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7745 (mp10) REVERT: D 414 MET cc_start: 0.6211 (mtm) cc_final: 0.5279 (pmm) REVERT: D 496 MET cc_start: 0.2673 (ttm) cc_final: 0.1672 (tmm) REVERT: E 5 ASP cc_start: 0.5917 (OUTLIER) cc_final: 0.5595 (p0) REVERT: E 56 GLU cc_start: 0.8315 (pp20) cc_final: 0.7423 (pp20) REVERT: E 95 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9116 (tm-30) REVERT: E 102 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8386 (tpt90) REVERT: E 174 TYR cc_start: 0.8816 (p90) cc_final: 0.8551 (p90) REVERT: F 10 MET cc_start: 0.9276 (mmm) cc_final: 0.9066 (mmm) REVERT: F 81 ASP cc_start: 0.9136 (t0) cc_final: 0.8779 (t0) REVERT: F 95 GLU cc_start: 0.9008 (tp30) cc_final: 0.8721 (tp30) REVERT: G 60 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.8508 (p90) REVERT: H 5 ASP cc_start: 0.6054 (m-30) cc_final: 0.5696 (m-30) REVERT: H 9 GLN cc_start: 0.8593 (mt0) cc_final: 0.8081 (mp10) REVERT: H 78 LYS cc_start: 0.8855 (ptmt) cc_final: 0.8524 (pttm) REVERT: H 203 ASP cc_start: 0.9447 (OUTLIER) cc_final: 0.9205 (t0) outliers start: 85 outliers final: 48 residues processed: 248 average time/residue: 1.3783 time to fit residues: 384.6697 Evaluate side-chains 213 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 159 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 42 optimal weight: 50.0000 chunk 127 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 216 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 113 optimal weight: 20.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 569 ASN D 619 ASN G 160 ASN G 205 HIS ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18420 Z= 0.351 Angle : 0.653 13.799 24809 Z= 0.334 Chirality : 0.043 0.263 2768 Planarity : 0.004 0.047 3018 Dihedral : 10.575 89.603 2812 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.49 % Favored : 96.29 % Rotamer: Outliers : 4.73 % Allowed : 21.40 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.35 (0.19), residues: 2235 helix: 2.44 (0.14), residues: 1340 sheet: -2.33 (0.37), residues: 143 loop : -1.38 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 766 HIS 0.005 0.001 HIS E 60 PHE 0.018 0.002 PHE D 623 TYR 0.020 0.002 TYR C 711 ARG 0.007 0.001 ARG G 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 171 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.4278 (mpp) cc_final: 0.2950 (mpp) REVERT: A 503 MET cc_start: 0.7666 (ttm) cc_final: 0.7389 (ptm) REVERT: A 756 GLN cc_start: 0.5954 (OUTLIER) cc_final: 0.5213 (pp30) REVERT: B 408 MET cc_start: 0.6772 (mmm) cc_final: 0.6368 (mpp) REVERT: B 496 MET cc_start: 0.1985 (ptp) cc_final: 0.1042 (ppp) REVERT: B 586 ARG cc_start: 0.9283 (mmm-85) cc_final: 0.8886 (mmm160) REVERT: C 414 MET cc_start: 0.7506 (mtm) cc_final: 0.6344 (ptt) REVERT: C 463 MET cc_start: 0.3172 (mpp) cc_final: 0.2522 (tpp) REVERT: C 496 MET cc_start: 0.4213 (mtt) cc_final: 0.2772 (tpt) REVERT: C 708 MET cc_start: 0.3508 (pmt) cc_final: 0.3087 (pmm) REVERT: C 714 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7768 (mp10) REVERT: D 408 MET cc_start: 0.4521 (tpp) cc_final: 0.4140 (tpp) REVERT: D 496 MET cc_start: 0.2520 (ttm) cc_final: 0.1621 (tmm) REVERT: E 56 GLU cc_start: 0.8283 (pp20) cc_final: 0.8067 (pp20) REVERT: E 95 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9115 (tm-30) REVERT: E 102 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8318 (tpt90) REVERT: E 174 TYR cc_start: 0.8909 (p90) cc_final: 0.8682 (p90) REVERT: F 10 MET cc_start: 0.9369 (mmm) cc_final: 0.9115 (mmm) REVERT: F 81 ASP cc_start: 0.9131 (t0) cc_final: 0.8744 (t0) REVERT: F 95 GLU cc_start: 0.9034 (tp30) cc_final: 0.8698 (tp30) REVERT: G 60 HIS cc_start: 0.8841 (OUTLIER) cc_final: 0.8454 (p90) REVERT: H 9 GLN cc_start: 0.8712 (mt0) cc_final: 0.8129 (mp10) REVERT: H 203 ASP cc_start: 0.9437 (OUTLIER) cc_final: 0.9214 (t0) outliers start: 86 outliers final: 55 residues processed: 239 average time/residue: 1.3017 time to fit residues: 352.6821 Evaluate side-chains 213 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 154 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 0.0000 chunk 158 optimal weight: 0.4980 chunk 122 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 121 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 135 optimal weight: 0.0970 chunk 131 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 569 ASN D 619 ASN E 160 ASN F 60 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18420 Z= 0.160 Angle : 0.605 13.395 24809 Z= 0.304 Chirality : 0.041 0.454 2768 Planarity : 0.004 0.047 3018 Dihedral : 9.887 89.917 2808 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.00 % Favored : 96.78 % Rotamer: Outliers : 4.02 % Allowed : 22.39 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 (0.19), residues: 2235 helix: 2.71 (0.14), residues: 1335 sheet: -2.25 (0.42), residues: 112 loop : -1.40 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 766 HIS 0.004 0.001 HIS F 205 PHE 0.015 0.001 PHE D 623 TYR 0.028 0.001 TYR C 711 ARG 0.008 0.001 ARG G 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 192 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.4678 (mpp) cc_final: 0.3982 (mpp) REVERT: A 670 MET cc_start: 0.7025 (mmp) cc_final: 0.6329 (mmm) REVERT: A 756 GLN cc_start: 0.5641 (OUTLIER) cc_final: 0.4858 (pp30) REVERT: B 496 MET cc_start: 0.1302 (ptp) cc_final: 0.0739 (ppp) REVERT: B 586 ARG cc_start: 0.9096 (mmm-85) cc_final: 0.8695 (mmm160) REVERT: B 708 MET cc_start: 0.5569 (mpp) cc_final: 0.5312 (mpp) REVERT: C 414 MET cc_start: 0.7722 (mtm) cc_final: 0.6269 (ptt) REVERT: C 463 MET cc_start: 0.3125 (mpp) cc_final: 0.2470 (tpp) REVERT: C 496 MET cc_start: 0.4204 (mtt) cc_final: 0.2942 (tpt) REVERT: C 586 ARG cc_start: 0.9025 (ttm110) cc_final: 0.8752 (ttm110) REVERT: C 647 TYR cc_start: 0.2609 (p90) cc_final: 0.2304 (p90) REVERT: C 714 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7687 (mp10) REVERT: C 721 MET cc_start: 0.8886 (ptm) cc_final: 0.8230 (pmt) REVERT: D 414 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5219 (pmm) REVERT: D 496 MET cc_start: 0.2208 (OUTLIER) cc_final: 0.1390 (tmm) REVERT: E 5 ASP cc_start: 0.5636 (OUTLIER) cc_final: 0.5083 (p0) REVERT: E 13 THR cc_start: 0.8951 (m) cc_final: 0.8673 (t) REVERT: E 56 GLU cc_start: 0.8460 (pp20) cc_final: 0.8095 (pp20) REVERT: E 95 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9105 (tm-30) REVERT: E 102 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8494 (tpt90) REVERT: E 174 TYR cc_start: 0.8768 (p90) cc_final: 0.8515 (p90) REVERT: F 81 ASP cc_start: 0.9126 (t0) cc_final: 0.8742 (t0) REVERT: F 95 GLU cc_start: 0.9169 (tp30) cc_final: 0.8858 (tp30) REVERT: G 56 GLU cc_start: 0.8569 (tp30) cc_final: 0.7900 (tp30) REVERT: H 9 GLN cc_start: 0.8601 (mt0) cc_final: 0.8246 (mp10) outliers start: 73 outliers final: 45 residues processed: 247 average time/residue: 1.2860 time to fit residues: 357.3720 Evaluate side-chains 212 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 162 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.5980 chunk 86 optimal weight: 50.0000 chunk 128 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 40.0000 chunk 41 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 569 ASN D 619 ASN E 160 ASN G 205 HIS ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18420 Z= 0.273 Angle : 0.656 13.326 24809 Z= 0.331 Chirality : 0.042 0.355 2768 Planarity : 0.004 0.047 3018 Dihedral : 9.999 89.730 2808 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.31 % Favored : 96.47 % Rotamer: Outliers : 4.02 % Allowed : 22.83 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.57 (0.19), residues: 2235 helix: 2.64 (0.14), residues: 1335 sheet: -2.30 (0.40), residues: 117 loop : -1.37 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A 766 HIS 0.004 0.001 HIS E 60 PHE 0.015 0.001 PHE F 73 TYR 0.031 0.001 TYR C 711 ARG 0.009 0.001 ARG E 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 174 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 674 MET cc_start: 0.7941 (mpp) cc_final: 0.7480 (mpt) REVERT: A 756 GLN cc_start: 0.5543 (OUTLIER) cc_final: 0.4702 (pp30) REVERT: B 496 MET cc_start: 0.1341 (ptp) cc_final: 0.0674 (ppp) REVERT: B 586 ARG cc_start: 0.9264 (mmm-85) cc_final: 0.8889 (mmm160) REVERT: B 769 ASP cc_start: 0.7366 (t0) cc_final: 0.7098 (m-30) REVERT: C 414 MET cc_start: 0.7715 (mtm) cc_final: 0.6281 (ptt) REVERT: C 463 MET cc_start: 0.3172 (mpp) cc_final: 0.2520 (tpp) REVERT: C 496 MET cc_start: 0.4083 (mtt) cc_final: 0.2718 (mmp) REVERT: C 708 MET cc_start: 0.3264 (pmt) cc_final: 0.3005 (pmm) REVERT: C 714 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7758 (mp10) REVERT: C 721 MET cc_start: 0.8952 (ptm) cc_final: 0.8314 (pmt) REVERT: D 408 MET cc_start: 0.4654 (tpp) cc_final: 0.4234 (tpp) REVERT: D 414 MET cc_start: 0.5931 (OUTLIER) cc_final: 0.5145 (pmm) REVERT: D 496 MET cc_start: 0.2076 (OUTLIER) cc_final: 0.1156 (tmm) REVERT: E 5 ASP cc_start: 0.5944 (OUTLIER) cc_final: 0.5602 (p0) REVERT: E 37 ARG cc_start: 0.9377 (tpt90) cc_final: 0.9074 (tpt90) REVERT: E 95 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9049 (tp30) REVERT: E 102 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8445 (tpt90) REVERT: E 174 TYR cc_start: 0.8782 (p90) cc_final: 0.8575 (p90) REVERT: F 81 ASP cc_start: 0.9090 (t0) cc_final: 0.8676 (t0) REVERT: F 95 GLU cc_start: 0.9187 (tp30) cc_final: 0.8870 (tp30) REVERT: G 56 GLU cc_start: 0.8628 (tp30) cc_final: 0.8367 (tp30) REVERT: G 58 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8627 (mmp) REVERT: H 9 GLN cc_start: 0.8852 (mt0) cc_final: 0.8518 (mp10) outliers start: 73 outliers final: 43 residues processed: 230 average time/residue: 1.3238 time to fit residues: 342.6208 Evaluate side-chains 213 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 164 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.2980 chunk 206 optimal weight: 3.9990 chunk 188 optimal weight: 0.5980 chunk 201 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 61 optimal weight: 20.0000 chunk 181 optimal weight: 0.6980 chunk 190 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 ASN D 569 ASN D 619 ASN E 160 ASN F 60 HIS ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18420 Z= 0.175 Angle : 0.647 13.233 24809 Z= 0.323 Chirality : 0.041 0.369 2768 Planarity : 0.004 0.049 3018 Dihedral : 9.587 88.787 2808 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.86 % Favored : 96.91 % Rotamer: Outliers : 2.97 % Allowed : 23.54 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.64 (0.19), residues: 2235 helix: 2.72 (0.14), residues: 1335 sheet: -2.25 (0.39), residues: 116 loop : -1.40 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP D 766 HIS 0.006 0.001 HIS A 412 PHE 0.018 0.001 PHE C 682 TYR 0.030 0.001 TYR C 711 ARG 0.009 0.001 ARG E 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 182 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 674 MET cc_start: 0.7672 (mpp) cc_final: 0.7146 (mpt) REVERT: A 756 GLN cc_start: 0.5518 (OUTLIER) cc_final: 0.4860 (pp30) REVERT: B 408 MET cc_start: 0.5952 (mpm) cc_final: 0.3553 (pp-130) REVERT: B 463 MET cc_start: -0.2271 (ptt) cc_final: -0.2502 (mpp) REVERT: B 496 MET cc_start: 0.1806 (ptp) cc_final: 0.0957 (ppp) REVERT: B 586 ARG cc_start: 0.9134 (mmm-85) cc_final: 0.8689 (mmm160) REVERT: B 769 ASP cc_start: 0.7334 (t0) cc_final: 0.7129 (m-30) REVERT: C 414 MET cc_start: 0.7776 (mtm) cc_final: 0.6673 (ptt) REVERT: C 463 MET cc_start: 0.3151 (mpp) cc_final: 0.2482 (tpp) REVERT: C 496 MET cc_start: 0.4001 (mtt) cc_final: 0.2630 (mmp) REVERT: C 670 MET cc_start: 0.6459 (pmm) cc_final: 0.5880 (mpp) REVERT: C 708 MET cc_start: 0.3381 (pmt) cc_final: 0.3125 (pmm) REVERT: C 714 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7462 (mp10) REVERT: C 721 MET cc_start: 0.8959 (ptm) cc_final: 0.8383 (pmt) REVERT: D 408 MET cc_start: 0.4424 (tpp) cc_final: 0.4099 (tpp) REVERT: D 414 MET cc_start: 0.6336 (mtm) cc_final: 0.5428 (pmm) REVERT: D 496 MET cc_start: 0.1901 (OUTLIER) cc_final: 0.1069 (tmm) REVERT: D 670 MET cc_start: 0.7497 (ppp) cc_final: 0.7092 (ppp) REVERT: E 5 ASP cc_start: 0.5712 (OUTLIER) cc_final: 0.5203 (p0) REVERT: E 13 THR cc_start: 0.8963 (m) cc_final: 0.8703 (t) REVERT: E 95 GLU cc_start: 0.9383 (mm-30) cc_final: 0.9047 (tp30) REVERT: E 102 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8515 (tpt90) REVERT: F 81 ASP cc_start: 0.9089 (t0) cc_final: 0.8706 (t0) REVERT: F 95 GLU cc_start: 0.9179 (tp30) cc_final: 0.8834 (tp30) REVERT: G 56 GLU cc_start: 0.8592 (tp30) cc_final: 0.8357 (tp30) REVERT: H 9 GLN cc_start: 0.8928 (mt0) cc_final: 0.8689 (mp10) outliers start: 54 outliers final: 37 residues processed: 224 average time/residue: 1.2175 time to fit residues: 309.8624 Evaluate side-chains 216 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 175 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.0980 chunk 212 optimal weight: 0.0870 chunk 129 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 223 optimal weight: 3.9990 chunk 205 optimal weight: 0.0770 chunk 177 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 569 ASN D 619 ASN E 160 ASN F 60 HIS G 205 HIS H 79 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18420 Z= 0.183 Angle : 0.664 12.808 24809 Z= 0.330 Chirality : 0.041 0.343 2768 Planarity : 0.004 0.047 3018 Dihedral : 9.335 88.238 2808 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.09 % Favored : 96.69 % Rotamer: Outliers : 2.48 % Allowed : 24.48 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.71 (0.19), residues: 2235 helix: 2.74 (0.14), residues: 1336 sheet: -1.89 (0.40), residues: 131 loop : -1.33 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP D 766 HIS 0.005 0.001 HIS A 412 PHE 0.017 0.001 PHE D 623 TYR 0.030 0.001 TYR C 711 ARG 0.011 0.001 ARG E 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 182 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 674 MET cc_start: 0.7679 (mpp) cc_final: 0.7173 (mpt) REVERT: A 756 GLN cc_start: 0.5136 (OUTLIER) cc_final: 0.4311 (pp30) REVERT: B 496 MET cc_start: 0.1269 (ptp) cc_final: 0.0494 (ppp) REVERT: B 586 ARG cc_start: 0.9143 (mmm-85) cc_final: 0.8701 (mmm160) REVERT: B 721 MET cc_start: 0.7843 (pmm) cc_final: 0.7459 (pmm) REVERT: C 414 MET cc_start: 0.7753 (mtm) cc_final: 0.6670 (ptt) REVERT: C 463 MET cc_start: 0.3142 (mpp) cc_final: 0.2482 (tpp) REVERT: C 496 MET cc_start: 0.4162 (mtt) cc_final: 0.2772 (mmp) REVERT: C 708 MET cc_start: 0.3388 (pmt) cc_final: 0.3137 (pmm) REVERT: C 721 MET cc_start: 0.8961 (ptm) cc_final: 0.8390 (pmt) REVERT: D 408 MET cc_start: 0.4110 (tpp) cc_final: 0.3856 (tpp) REVERT: D 414 MET cc_start: 0.6341 (mtm) cc_final: 0.5421 (pmm) REVERT: D 496 MET cc_start: 0.1944 (OUTLIER) cc_final: 0.0943 (tmm) REVERT: E 5 ASP cc_start: 0.5957 (OUTLIER) cc_final: 0.5690 (p0) REVERT: E 56 GLU cc_start: 0.8507 (pp20) cc_final: 0.8098 (pp20) REVERT: E 95 GLU cc_start: 0.9379 (mm-30) cc_final: 0.9043 (tp30) REVERT: E 102 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8559 (tpt90) REVERT: F 81 ASP cc_start: 0.9054 (t0) cc_final: 0.8656 (t0) REVERT: F 95 GLU cc_start: 0.9177 (tp30) cc_final: 0.8853 (tp30) REVERT: G 58 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8896 (mmp) REVERT: H 9 GLN cc_start: 0.8878 (mt0) cc_final: 0.8651 (mp10) outliers start: 45 outliers final: 30 residues processed: 217 average time/residue: 1.2594 time to fit residues: 308.8614 Evaluate side-chains 205 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.0870 chunk 189 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 182 optimal weight: 0.5980 chunk 22 optimal weight: 0.0170 chunk 32 optimal weight: 10.0000 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 ASN D 569 ASN D 619 ASN E 160 ASN G 205 HIS ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.160651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085659 restraints weight = 35816.019| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.65 r_work: 0.3080 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18420 Z= 0.217 Angle : 0.677 12.369 24809 Z= 0.335 Chirality : 0.042 0.340 2768 Planarity : 0.004 0.046 3018 Dihedral : 9.296 88.376 2808 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.00 % Favored : 96.78 % Rotamer: Outliers : 2.31 % Allowed : 24.81 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.72 (0.19), residues: 2235 helix: 2.75 (0.14), residues: 1336 sheet: -2.17 (0.37), residues: 141 loop : -1.25 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP D 766 HIS 0.004 0.001 HIS A 412 PHE 0.016 0.001 PHE D 623 TYR 0.030 0.001 TYR C 711 ARG 0.009 0.001 ARG E 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7088.94 seconds wall clock time: 141 minutes 24.65 seconds (8484.65 seconds total)