Starting phenix.real_space_refine on Sun Sep 29 00:31:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss3_40742/09_2024/8ss3_40742.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss3_40742/09_2024/8ss3_40742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss3_40742/09_2024/8ss3_40742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss3_40742/09_2024/8ss3_40742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss3_40742/09_2024/8ss3_40742.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss3_40742/09_2024/8ss3_40742.cif" } resolution = 3.21 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= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 S 130 5.16 5 C 13297 2.51 5 N 2919 2.21 5 O 3499 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19887 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4671 Classifications: {'peptide': 596} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 578} Chain breaks: 4 Chain: "B" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "C" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4671 Classifications: {'peptide': 596} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 578} Chain breaks: 4 Chain: "D" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 613 Unusual residues: {'AJP': 3, 'CLR': 2, 'PCW': 12, 'SPD': 1, 'ZK1': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 512 Unresolved non-hydrogen dihedrals: 543 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 358 Unusual residues: {'PCW': 10, 'ZK1': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 449 Unusual residues: {'AJP': 3, 'CLR': 2, 'PCW': 9, 'ZK1': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 307 Unusual residues: {'PCW': 9, 'ZK1': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 47 Chain: "E" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {'PCW': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 4, 'PCW:plan-2': 1, 'PCW:plan-3': 4, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 49 Chain: "F" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {'PCW': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 4, 'PCW:plan-2': 1, 'PCW:plan-3': 4, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 11.83, per 1000 atoms: 0.59 Number of scatterers: 19887 At special positions: 0 Unit cell: (118.69, 130.31, 138.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 130 16.00 P 30 15.00 F 12 9.00 O 3499 8.00 N 2919 7.00 C 13297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " 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=2.01 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 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: 4.35 Conformation dependent library (CDL) restraints added in 2.4 seconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4208 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 57.4% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.980A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 435 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.534A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 543 removed outlier: 3.831A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.631A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 630 removed outlier: 3.862A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 642 Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.588A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.829A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 743 through 756 Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.763A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 822 removed outlier: 3.544A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 819 " --> pdb=" O CYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 858 removed outlier: 3.526A pdb=" N SER A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 952 removed outlier: 3.995A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 986 removed outlier: 3.676A pdb=" N PHE A 960 " --> pdb=" O THR A 956 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1033 removed outlier: 3.732A pdb=" N PHE A1009 " --> pdb=" O TRP A1005 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A1025 " --> pdb=" O GLY A1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.594A pdb=" N ALA B 429 " --> pdb=" O CYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.510A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 546 removed outlier: 3.525A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.643A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.661A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 665 through 677 removed outlier: 4.086A pdb=" N LYS B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.644A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 767 removed outlier: 3.511A pdb=" N TRP B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.848A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.980A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.534A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 543 removed outlier: 3.831A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.631A pdb=" N SER C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 630 removed outlier: 3.863A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 642 Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.588A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.828A 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 706 through 714 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 743 through 756 Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.763A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 822 removed outlier: 3.545A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 819 " --> pdb=" O CYS C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 858 removed outlier: 3.526A pdb=" N SER C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 952 removed outlier: 3.996A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 986 removed outlier: 3.677A pdb=" N PHE C 960 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 962 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP C 986 " --> pdb=" O SER C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1033 removed outlier: 3.731A pdb=" N PHE C1009 " --> pdb=" O TRP C1005 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C1025 " --> pdb=" O GLY C1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.595A pdb=" N ALA D 429 " --> pdb=" O CYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 removed outlier: 3.509A pdb=" N TYR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 546 removed outlier: 3.525A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.643A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.661A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 665 through 677 removed outlier: 4.086A pdb=" N LYS D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.643A 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 767 removed outlier: 3.512A pdb=" N TRP D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.849A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 37 removed outlier: 3.892A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE E 31 " --> pdb=" O HIS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.675A pdb=" N LEU E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 65 " --> pdb=" O CYS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 85 removed outlier: 3.598A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY E 76 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 107 removed outlier: 3.614A pdb=" N ASN E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 124 through 159 removed outlier: 3.626A pdb=" N TRP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 37 removed outlier: 3.892A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE F 31 " --> pdb=" O HIS F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.675A pdb=" N LEU F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG F 65 " --> pdb=" O CYS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 85 removed outlier: 3.598A pdb=" N HIS F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 107 removed outlier: 3.614A pdb=" N ASN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 124 through 159 removed outlier: 3.627A pdb=" N TRP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 removed outlier: 6.418A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 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 490 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.073A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 682 through 683 removed outlier: 7.455A pdb=" N VAL A 683 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR A 649 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 10.821A pdb=" N LEU A 650 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 875 through 880 removed outlier: 6.547A pdb=" N GLU A 866 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 865 " --> pdb=" O ASN A1000 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 998 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 890 Processing sheet with id=AA8, first strand: chain 'B' and resid 394 through 399 removed outlier: 6.723A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB1, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB2, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.864A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 702 through 705 removed outlier: 4.383A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.418A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AB7, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.073A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 682 through 683 removed outlier: 7.455A pdb=" N VAL C 683 " --> pdb=" O TYR C 647 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR C 649 " --> pdb=" O VAL C 683 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N LEU C 650 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 875 through 880 removed outlier: 6.547A pdb=" N GLU C 866 " --> pdb=" O LYS C 879 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 865 " --> pdb=" O ASN C1000 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR C 998 " --> pdb=" O GLY C 867 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 888 through 890 Processing sheet with id=AC2, first strand: chain 'D' and resid 394 through 399 removed outlier: 6.723A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC4, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC5, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.864A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 702 through 705 removed outlier: 4.384A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2808 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: 5.62 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.02 - 0.46: 5 0.46 - 0.90: 6 0.90 - 1.34: 5363 1.34 - 1.78: 14681 1.78 - 2.22: 253 Warning: very small bond lengths. Bond restraints: 20308 Sorted by residual: bond pdb=" C27 AJP C1110 " pdb=" O78 AJP C1110 " ideal model delta sigma weight residual 1.406 0.016 1.390 2.00e-02 2.50e+03 4.83e+03 bond pdb=" C27 AJP A1111 " pdb=" O78 AJP A1111 " ideal model delta sigma weight residual 1.406 0.048 1.358 2.00e-02 2.50e+03 4.61e+03 bond pdb=" C27 AJP C1114 " pdb=" O78 AJP C1114 " ideal model delta sigma weight residual 1.406 0.058 1.348 2.00e-02 2.50e+03 4.54e+03 bond pdb=" C27 AJP A1110 " pdb=" O78 AJP A1110 " ideal model delta sigma weight residual 1.406 0.070 1.336 2.00e-02 2.50e+03 4.46e+03 bond pdb=" C27 AJP A1116 " pdb=" O78 AJP A1116 " ideal model delta sigma weight residual 1.406 0.088 1.318 2.00e-02 2.50e+03 4.34e+03 ... (remaining 20303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.71: 26292 4.71 - 9.41: 799 9.41 - 14.12: 152 14.12 - 18.82: 15 18.82 - 23.53: 6 Bond angle restraints: 27264 Sorted by residual: angle pdb=" C17 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C18 CLR A1107 " ideal model delta sigma weight residual 110.18 86.65 23.53 3.00e+00 1.11e-01 6.15e+01 angle pdb=" C17 CLR C1106 " pdb=" C13 CLR C1106 " pdb=" C18 CLR C1106 " ideal model delta sigma weight residual 110.18 86.77 23.41 3.00e+00 1.11e-01 6.09e+01 angle pdb=" C17 CLR A1112 " pdb=" C13 CLR A1112 " pdb=" C18 CLR A1112 " ideal model delta sigma weight residual 110.18 88.52 21.66 3.00e+00 1.11e-01 5.21e+01 angle pdb=" N VAL B 514 " pdb=" CA VAL B 514 " pdb=" C VAL B 514 " ideal model delta sigma weight residual 112.83 105.74 7.09 9.90e-01 1.02e+00 5.14e+01 angle pdb=" N VAL D 514 " pdb=" CA VAL D 514 " pdb=" C VAL D 514 " ideal model delta sigma weight residual 112.83 105.74 7.09 9.90e-01 1.02e+00 5.13e+01 ... (remaining 27259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 12006 35.97 - 71.94: 635 71.94 - 107.91: 187 107.91 - 143.88: 97 143.88 - 179.85: 48 Dihedral angle restraints: 12973 sinusoidal: 6391 harmonic: 6582 Sorted by residual: dihedral pdb=" CA PRO F 109 " pdb=" C PRO F 109 " pdb=" N ALA F 110 " pdb=" CA ALA F 110 " ideal model delta harmonic sigma weight residual -180.00 -118.55 -61.45 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA PRO E 109 " pdb=" C PRO E 109 " pdb=" N ALA E 110 " pdb=" CA ALA E 110 " ideal model delta harmonic sigma weight residual -180.00 -118.58 -61.42 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA MET E 116 " pdb=" C MET E 116 " pdb=" N TYR E 117 " pdb=" CA TYR E 117 " ideal model delta harmonic sigma weight residual 180.00 120.86 59.14 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 12970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.098: 2878 1.098 - 2.196: 14 2.196 - 3.294: 11 3.294 - 4.392: 16 4.392 - 5.489: 42 Chirality restraints: 2961 Sorted by residual: chirality pdb=" C15 AJP A1110 " pdb=" C14 AJP A1110 " pdb=" C16 AJP A1110 " pdb=" C20 AJP A1110 " both_signs ideal model delta sigma weight residual False -2.42 3.07 -5.49 2.00e-01 2.50e+01 7.53e+02 chirality pdb=" C15 AJP C1109 " pdb=" C14 AJP C1109 " pdb=" C16 AJP C1109 " pdb=" C20 AJP C1109 " both_signs ideal model delta sigma weight residual False -2.42 3.07 -5.49 2.00e-01 2.50e+01 7.53e+02 chirality pdb=" C02 AJP A1110 " pdb=" C01 AJP A1110 " pdb=" C03 AJP A1110 " pdb=" C85 AJP A1110 " both_signs ideal model delta sigma weight residual False 2.60 -2.84 5.44 2.00e-01 2.50e+01 7.40e+02 ... (remaining 2958 not shown) Planarity restraints: 3162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 116 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C MET E 116 " -0.048 2.00e-02 2.50e+03 pdb=" O MET E 116 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR E 117 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 116 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C MET F 116 " 0.048 2.00e-02 2.50e+03 pdb=" O MET F 116 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR F 117 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 406 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C VAL D 406 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL D 406 " -0.017 2.00e-02 2.50e+03 pdb=" N MET D 407 " -0.015 2.00e-02 2.50e+03 ... (remaining 3159 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 530 2.68 - 3.23: 17707 3.23 - 3.79: 29684 3.79 - 4.34: 41312 4.34 - 4.90: 68155 Nonbonded interactions: 157388 Sorted by model distance: nonbonded pdb=" OE2 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.123 3.040 nonbonded pdb=" OE2 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.123 3.040 nonbonded pdb=" O25 AJP A1111 " pdb=" O79 AJP A1111 " model vdw 2.172 2.432 nonbonded pdb=" O25 AJP C1110 " pdb=" O79 AJP C1110 " model vdw 2.176 2.432 nonbonded pdb=" O31 AJP A1110 " pdb=" O78 AJP A1110 " model vdw 2.196 2.432 ... (remaining 157383 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 392 through 1035 or resid 1101 through 1104 or (resid 1105 \ and (name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C20 or name C21 or name C22 or name C23)) or resid 1108 or resid \ 1110 or (resid 1113 and (name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23)) or r \ esid 1115)) selection = (chain 'C' and (resid 392 through 1035 or resid 1101 through 1105 or resid 1108 \ or resid 1110 or resid 1113 or resid 1115)) } ncs_group { reference = (chain 'B' and (resid 392 through 820 or resid 1101 through 1109 or (resid 1110 \ and (name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22 or name C23)))) selection = (chain 'D' and (resid 392 through 820 or resid 1101 through 1108 or (resid 1109 \ through 1110 and (name C13 or name C14 or name C15 or name C16 or name C17 or na \ me C18 or name C19 or name C20 or name C21 or name C22 or name C23)))) } ncs_group { reference = (chain 'E' and (resid 2 through 159 or resid 201 or (resid 202 and (name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ )) or resid 204 through 205)) selection = (chain 'F' and (resid 2 through 159 or resid 201 or (resid 202 and (name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ )) or resid 204 through 205)) } 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 41.130 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.047 1.390 20308 Z= 2.740 Angle : 1.899 23.526 27264 Z= 0.848 Chirality : 0.688 5.489 2961 Planarity : 0.007 0.062 3162 Dihedral : 28.238 179.849 8747 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.59 % Favored : 91.70 % Rotamer: Outliers : 0.52 % Allowed : 3.92 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.82 % 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: -6.01 (0.11), residues: 2240 helix: -4.03 (0.07), residues: 1304 sheet: -3.28 (0.29), residues: 216 loop : -3.62 (0.17), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 861 HIS 0.007 0.002 HIS E 27 PHE 0.033 0.003 PHE A 574 TYR 0.033 0.003 TYR C 702 ARG 0.006 0.001 ARG C 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 511 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 663 LYS cc_start: 0.8768 (mptp) cc_final: 0.8485 (mttt) REVERT: A 674 MET cc_start: 0.8782 (mtm) cc_final: 0.8517 (mtp) REVERT: A 1005 TRP cc_start: 0.8230 (p-90) cc_final: 0.7932 (p-90) REVERT: B 638 ASP cc_start: 0.8032 (m-30) cc_final: 0.7796 (m-30) REVERT: B 642 GLN cc_start: 0.8075 (pp30) cc_final: 0.7471 (pp30) REVERT: C 519 ASP cc_start: 0.8612 (m-30) cc_final: 0.8408 (m-30) REVERT: C 630 VAL cc_start: 0.8564 (t) cc_final: 0.8361 (m) REVERT: C 674 MET cc_start: 0.8866 (mtm) cc_final: 0.8641 (mtp) REVERT: C 1005 TRP cc_start: 0.8137 (p-90) cc_final: 0.7896 (p-90) REVERT: D 527 MET cc_start: 0.7638 (mmm) cc_final: 0.7387 (mmt) REVERT: D 657 GLU cc_start: 0.7760 (tp30) cc_final: 0.7496 (mm-30) REVERT: D 661 ARG cc_start: 0.7850 (ptt180) cc_final: 0.7637 (ttp-170) REVERT: D 770 LYS cc_start: 0.7660 (mmtp) cc_final: 0.7437 (tttp) REVERT: F 64 LEU cc_start: 0.8041 (mt) cc_final: 0.7837 (mt) outliers start: 10 outliers final: 0 residues processed: 519 average time/residue: 0.3306 time to fit residues: 254.8787 Evaluate side-chains 295 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 131 optimal weight: 0.0980 chunk 205 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 508 GLN A 575 ASN A 747 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 ASN B 461 ASN B 586 GLN B 587 GLN C 412 HIS C 575 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN D 586 GLN D 587 GLN E 75 HIS E 94 ASN E 124 ASN E 132 GLN F 94 ASN F 124 ASN F 132 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20308 Z= 0.221 Angle : 1.320 31.650 27264 Z= 0.521 Chirality : 0.151 2.436 2961 Planarity : 0.006 0.062 3162 Dihedral : 28.284 179.176 4619 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.65 % Favored : 92.95 % Rotamer: Outliers : 2.68 % Allowed : 8.97 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.15), residues: 2240 helix: -1.32 (0.12), residues: 1320 sheet: -2.71 (0.32), residues: 194 loop : -3.41 (0.18), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 766 HIS 0.008 0.001 HIS C 412 PHE 0.022 0.002 PHE D 541 TYR 0.018 0.002 TYR C 702 ARG 0.007 0.000 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 322 time to evaluate : 2.098 Fit side-chains revert: symmetry clash REVERT: A 663 LYS cc_start: 0.8792 (mptp) cc_final: 0.8475 (mttt) REVERT: A 669 LYS cc_start: 0.7641 (ttmt) cc_final: 0.7074 (mtpt) REVERT: A 860 TYR cc_start: 0.8015 (m-80) cc_final: 0.7694 (m-80) REVERT: A 880 MET cc_start: 0.7450 (tpp) cc_final: 0.7190 (tpp) REVERT: A 891 PHE cc_start: 0.7432 (m-80) cc_final: 0.7229 (m-80) REVERT: A 985 ASN cc_start: 0.7944 (m-40) cc_final: 0.7735 (m-40) REVERT: B 695 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6304 (mptt) REVERT: C 860 TYR cc_start: 0.8153 (m-80) cc_final: 0.7861 (m-80) REVERT: C 879 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8320 (mtpp) REVERT: C 957 ILE cc_start: 0.8011 (mm) cc_final: 0.7803 (mp) REVERT: C 998 TYR cc_start: 0.7567 (p90) cc_final: 0.7295 (p90) REVERT: D 439 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8287 (mmtm) REVERT: D 695 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.5487 (mptt) REVERT: D 706 SER cc_start: 0.8843 (t) cc_final: 0.8604 (p) REVERT: D 715 ARG cc_start: 0.7623 (tpp-160) cc_final: 0.7423 (mmt-90) REVERT: D 770 LYS cc_start: 0.7810 (mmtp) cc_final: 0.7526 (tttp) outliers start: 52 outliers final: 21 residues processed: 356 average time/residue: 0.3078 time to fit residues: 168.1412 Evaluate side-chains 305 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 282 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain F residue 122 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 205 optimal weight: 0.0020 chunk 222 optimal weight: 9.9990 chunk 183 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN C 412 HIS C 747 ASN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN D 587 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20308 Z= 0.290 Angle : 1.272 33.756 27264 Z= 0.496 Chirality : 0.145 2.405 2961 Planarity : 0.005 0.052 3162 Dihedral : 27.115 179.988 4619 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.14 % Favored : 92.50 % Rotamer: Outliers : 3.66 % Allowed : 10.15 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -1.65 (0.17), residues: 2240 helix: 0.27 (0.14), residues: 1310 sheet: -2.81 (0.31), residues: 198 loop : -3.10 (0.19), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 861 HIS 0.015 0.002 HIS C 883 PHE 0.019 0.002 PHE A 495 TYR 0.018 0.002 TYR B 702 ARG 0.009 0.001 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 296 time to evaluate : 2.698 Fit side-chains revert: symmetry clash REVERT: A 511 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8102 (tptp) REVERT: A 587 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.6526 (mm-40) REVERT: A 663 LYS cc_start: 0.8776 (mptp) cc_final: 0.8463 (mttt) REVERT: A 669 LYS cc_start: 0.7623 (ttmt) cc_final: 0.7090 (mtpt) REVERT: A 952 ARG cc_start: 0.6874 (ptp-170) cc_final: 0.6600 (ptp-170) REVERT: A 986 ASP cc_start: 0.7534 (p0) cc_final: 0.7330 (p0) REVERT: B 415 LEU cc_start: 0.7913 (mt) cc_final: 0.7695 (mt) REVERT: B 461 ASN cc_start: 0.7103 (t0) cc_final: 0.6632 (t0) REVERT: B 695 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.6354 (mptt) REVERT: B 721 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7976 (ttp) REVERT: C 585 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7699 (mmt) REVERT: C 860 TYR cc_start: 0.8183 (m-80) cc_final: 0.7738 (m-80) REVERT: C 877 GLU cc_start: 0.8055 (tt0) cc_final: 0.7812 (tt0) REVERT: C 879 LYS cc_start: 0.8676 (ttmt) cc_final: 0.8265 (mtpp) REVERT: C 985 ASN cc_start: 0.7759 (m-40) cc_final: 0.7521 (m110) REVERT: C 998 TYR cc_start: 0.7901 (p90) cc_final: 0.7604 (p90) REVERT: D 414 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7987 (ptp) REVERT: D 461 ASN cc_start: 0.7217 (t0) cc_final: 0.6705 (t0) REVERT: D 635 SER cc_start: 0.8582 (t) cc_final: 0.8091 (p) REVERT: D 695 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6141 (mptt) REVERT: D 764 ASN cc_start: 0.8095 (m110) cc_final: 0.7606 (m-40) REVERT: D 770 LYS cc_start: 0.7840 (mmtp) cc_final: 0.7619 (tttp) REVERT: E 148 TYR cc_start: 0.8338 (t80) cc_final: 0.8031 (t80) outliers start: 71 outliers final: 41 residues processed: 345 average time/residue: 0.3075 time to fit residues: 165.6950 Evaluate side-chains 322 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 275 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 195 optimal weight: 0.0980 chunk 58 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN C 412 HIS ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20308 Z= 0.198 Angle : 1.231 32.937 27264 Z= 0.473 Chirality : 0.143 2.303 2961 Planarity : 0.004 0.046 3162 Dihedral : 26.517 179.973 4619 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.79 % Favored : 92.86 % Rotamer: Outliers : 3.30 % Allowed : 11.55 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -0.81 (0.18), residues: 2240 helix: 1.04 (0.14), residues: 1314 sheet: -2.59 (0.32), residues: 198 loop : -2.94 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 766 HIS 0.011 0.002 HIS A 883 PHE 0.018 0.001 PHE C 999 TYR 0.017 0.001 TYR F 155 ARG 0.004 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 288 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 511 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8068 (tptp) REVERT: A 585 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8067 (mmt) REVERT: A 663 LYS cc_start: 0.8782 (mptp) cc_final: 0.8461 (mttt) REVERT: A 669 LYS cc_start: 0.7634 (ttmt) cc_final: 0.7130 (mtpt) REVERT: A 858 THR cc_start: 0.8829 (t) cc_final: 0.8562 (p) REVERT: A 952 ARG cc_start: 0.6893 (ptp-170) cc_final: 0.6603 (ptp-170) REVERT: A 985 ASN cc_start: 0.7500 (m-40) cc_final: 0.7293 (m110) REVERT: B 461 ASN cc_start: 0.7039 (t0) cc_final: 0.6733 (t0) REVERT: B 695 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6368 (mptt) REVERT: B 721 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7927 (ttp) REVERT: B 764 ASN cc_start: 0.8090 (m110) cc_final: 0.7581 (m-40) REVERT: C 585 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7664 (mmt) REVERT: C 708 MET cc_start: 0.8429 (mmp) cc_final: 0.8127 (mmp) REVERT: C 721 MET cc_start: 0.8621 (ptt) cc_final: 0.8381 (ptt) REVERT: C 860 TYR cc_start: 0.8148 (m-80) cc_final: 0.7890 (m-80) REVERT: C 879 LYS cc_start: 0.8664 (ttmt) cc_final: 0.8265 (mtpp) REVERT: C 985 ASN cc_start: 0.7670 (m-40) cc_final: 0.7393 (m110) REVERT: D 414 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7978 (ptp) REVERT: D 635 SER cc_start: 0.8450 (t) cc_final: 0.7938 (p) REVERT: D 695 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.5984 (mptt) REVERT: D 770 LYS cc_start: 0.7875 (mmtp) cc_final: 0.7646 (tttp) outliers start: 64 outliers final: 35 residues processed: 330 average time/residue: 0.2943 time to fit residues: 153.1272 Evaluate side-chains 309 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 268 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 196 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 764 ASN ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS C 764 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20308 Z= 0.231 Angle : 1.232 32.824 27264 Z= 0.473 Chirality : 0.142 2.253 2961 Planarity : 0.004 0.050 3162 Dihedral : 25.984 179.730 4619 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.23 % Favored : 92.41 % Rotamer: Outliers : 4.07 % Allowed : 11.65 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -0.39 (0.18), residues: 2240 helix: 1.39 (0.14), residues: 1316 sheet: -2.55 (0.33), residues: 190 loop : -2.78 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 766 HIS 0.009 0.002 HIS C 883 PHE 0.018 0.001 PHE B 438 TYR 0.015 0.002 TYR F 155 ARG 0.005 0.000 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 295 time to evaluate : 2.030 Fit side-chains REVERT: A 511 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8088 (tptp) REVERT: A 585 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8090 (mmt) REVERT: A 587 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.6415 (mm-40) REVERT: A 647 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: A 663 LYS cc_start: 0.8789 (mptp) cc_final: 0.8471 (mttt) REVERT: A 669 LYS cc_start: 0.7645 (ttmt) cc_final: 0.7091 (mtpt) REVERT: A 684 ARG cc_start: 0.8249 (ttm110) cc_final: 0.8031 (ttm110) REVERT: A 697 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8140 (pttp) REVERT: A 858 THR cc_start: 0.8871 (t) cc_final: 0.8611 (p) REVERT: A 952 ARG cc_start: 0.6921 (ptp-170) cc_final: 0.6585 (ptp-170) REVERT: A 985 ASN cc_start: 0.7584 (m-40) cc_final: 0.7304 (m110) REVERT: A 987 GLU cc_start: 0.6767 (tp30) cc_final: 0.6481 (tp30) REVERT: B 461 ASN cc_start: 0.7061 (t0) cc_final: 0.6639 (t0) REVERT: B 635 SER cc_start: 0.8453 (t) cc_final: 0.7923 (p) REVERT: B 695 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.6674 (mptt) REVERT: B 721 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7949 (ttp) REVERT: B 764 ASN cc_start: 0.8146 (m110) cc_final: 0.7675 (m-40) REVERT: C 585 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7687 (mmt) REVERT: C 663 LYS cc_start: 0.8838 (mttp) cc_final: 0.8416 (mttt) REVERT: C 669 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7219 (mtpt) REVERT: C 789 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8729 (tt) REVERT: C 860 TYR cc_start: 0.8148 (m-80) cc_final: 0.7910 (m-80) REVERT: C 879 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8394 (mtpt) REVERT: C 880 MET cc_start: 0.7512 (tpp) cc_final: 0.7108 (tpp) REVERT: C 901 PHE cc_start: 0.7188 (m-10) cc_final: 0.6867 (m-10) REVERT: C 985 ASN cc_start: 0.7596 (m-40) cc_final: 0.7312 (m110) REVERT: C 987 GLU cc_start: 0.6953 (tp30) cc_final: 0.6662 (tp30) REVERT: D 414 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7750 (ptp) REVERT: D 461 ASN cc_start: 0.7121 (t0) cc_final: 0.6661 (t0) REVERT: D 635 SER cc_start: 0.8427 (t) cc_final: 0.7942 (p) REVERT: D 695 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6211 (mptt) REVERT: D 770 LYS cc_start: 0.7909 (mmtp) cc_final: 0.7662 (tttp) REVERT: E 148 TYR cc_start: 0.8329 (t80) cc_final: 0.8018 (t80) outliers start: 79 outliers final: 42 residues processed: 347 average time/residue: 0.3193 time to fit residues: 174.2891 Evaluate side-chains 337 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 285 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20308 Z= 0.275 Angle : 1.240 32.947 27264 Z= 0.477 Chirality : 0.142 2.244 2961 Planarity : 0.004 0.046 3162 Dihedral : 25.713 179.829 4619 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.83 % Favored : 92.81 % Rotamer: Outliers : 3.97 % Allowed : 12.42 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -0.27 (0.18), residues: 2240 helix: 1.49 (0.14), residues: 1314 sheet: -2.61 (0.32), residues: 190 loop : -2.69 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 766 HIS 0.009 0.001 HIS A 883 PHE 0.017 0.002 PHE B 438 TYR 0.024 0.002 TYR E 155 ARG 0.006 0.000 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 294 time to evaluate : 1.944 Fit side-chains REVERT: A 511 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8117 (tptp) REVERT: A 585 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8087 (mmt) REVERT: A 587 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.6490 (mm-40) REVERT: A 647 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7542 (m-10) REVERT: A 663 LYS cc_start: 0.8817 (mptp) cc_final: 0.8502 (mttt) REVERT: A 669 LYS cc_start: 0.7671 (ttmt) cc_final: 0.7043 (mtpt) REVERT: A 952 ARG cc_start: 0.6965 (ptp-170) cc_final: 0.6619 (ptp-170) REVERT: A 985 ASN cc_start: 0.7493 (m-40) cc_final: 0.7202 (m110) REVERT: A 987 GLU cc_start: 0.6731 (tp30) cc_final: 0.6436 (tp30) REVERT: B 461 ASN cc_start: 0.7071 (t0) cc_final: 0.6710 (t0) REVERT: B 635 SER cc_start: 0.8448 (t) cc_final: 0.7956 (p) REVERT: B 695 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.6625 (mptt) REVERT: B 721 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7972 (ttp) REVERT: B 764 ASN cc_start: 0.8168 (m110) cc_final: 0.7674 (m-40) REVERT: C 503 MET cc_start: 0.8894 (ttp) cc_final: 0.8629 (ttm) REVERT: C 585 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.7715 (mmt) REVERT: C 634 GLU cc_start: 0.7612 (pt0) cc_final: 0.7350 (pm20) REVERT: C 663 LYS cc_start: 0.8860 (mttp) cc_final: 0.8449 (mttt) REVERT: C 669 LYS cc_start: 0.7716 (ttmt) cc_final: 0.7151 (mtpt) REVERT: C 860 TYR cc_start: 0.8154 (m-80) cc_final: 0.7922 (m-80) REVERT: C 879 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8294 (mtpt) REVERT: C 880 MET cc_start: 0.7687 (tpp) cc_final: 0.7375 (tpp) REVERT: C 901 PHE cc_start: 0.7163 (m-10) cc_final: 0.6858 (m-10) REVERT: C 952 ARG cc_start: 0.7020 (ptp-170) cc_final: 0.6767 (ptp-170) REVERT: C 985 ASN cc_start: 0.7623 (m-40) cc_final: 0.7269 (m110) REVERT: C 987 GLU cc_start: 0.6912 (tp30) cc_final: 0.6631 (tp30) REVERT: D 461 ASN cc_start: 0.7087 (t0) cc_final: 0.6761 (t0) REVERT: D 635 SER cc_start: 0.8391 (t) cc_final: 0.7892 (p) REVERT: D 695 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6364 (mptt) REVERT: D 770 LYS cc_start: 0.7957 (mmtp) cc_final: 0.7692 (tttp) REVERT: E 148 TYR cc_start: 0.8326 (t80) cc_final: 0.8007 (t80) outliers start: 77 outliers final: 54 residues processed: 346 average time/residue: 0.3012 time to fit residues: 160.7595 Evaluate side-chains 343 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 282 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 956 THR Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 159 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 217 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20308 Z= 0.211 Angle : 1.225 32.902 27264 Z= 0.469 Chirality : 0.142 2.232 2961 Planarity : 0.004 0.043 3162 Dihedral : 25.467 179.924 4619 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.05 % Favored : 92.59 % Rotamer: Outliers : 3.56 % Allowed : 13.45 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -0.05 (0.18), residues: 2240 helix: 1.67 (0.15), residues: 1314 sheet: -2.44 (0.33), residues: 190 loop : -2.61 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 766 HIS 0.011 0.002 HIS A 412 PHE 0.019 0.001 PHE B 438 TYR 0.019 0.001 TYR E 155 ARG 0.007 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 289 time to evaluate : 2.160 Fit side-chains REVERT: A 407 MET cc_start: 0.8434 (mtm) cc_final: 0.8227 (mtp) REVERT: A 511 LYS cc_start: 0.8424 (mmmt) cc_final: 0.8100 (tptp) REVERT: A 585 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8051 (mmt) REVERT: A 587 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.6437 (mm-40) REVERT: A 634 GLU cc_start: 0.7792 (pt0) cc_final: 0.7283 (pm20) REVERT: A 647 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7460 (m-10) REVERT: A 663 LYS cc_start: 0.8814 (mptp) cc_final: 0.8503 (mttt) REVERT: A 669 LYS cc_start: 0.7666 (ttmt) cc_final: 0.7062 (mtpt) REVERT: A 952 ARG cc_start: 0.6996 (ptp-170) cc_final: 0.6646 (ptp-170) REVERT: A 985 ASN cc_start: 0.7490 (m-40) cc_final: 0.7203 (m110) REVERT: B 461 ASN cc_start: 0.7058 (t0) cc_final: 0.6753 (t0) REVERT: B 635 SER cc_start: 0.8435 (t) cc_final: 0.7960 (p) REVERT: B 695 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.6724 (mptt) REVERT: B 721 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7967 (ttp) REVERT: B 764 ASN cc_start: 0.8208 (m110) cc_final: 0.7701 (m-40) REVERT: C 503 MET cc_start: 0.8917 (ttp) cc_final: 0.8648 (ttm) REVERT: C 585 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7690 (mmt) REVERT: C 634 GLU cc_start: 0.7634 (pt0) cc_final: 0.7322 (pm20) REVERT: C 663 LYS cc_start: 0.8850 (mttp) cc_final: 0.8443 (mttt) REVERT: C 669 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7134 (mtpt) REVERT: C 860 TYR cc_start: 0.8171 (m-80) cc_final: 0.7686 (m-80) REVERT: C 879 LYS cc_start: 0.8629 (ttmt) cc_final: 0.8321 (mtpt) REVERT: C 880 MET cc_start: 0.7660 (tpp) cc_final: 0.7389 (tpp) REVERT: C 901 PHE cc_start: 0.7178 (m-10) cc_final: 0.6828 (m-10) REVERT: C 952 ARG cc_start: 0.7017 (ptp-170) cc_final: 0.6756 (ptp-170) REVERT: C 985 ASN cc_start: 0.7562 (m-40) cc_final: 0.7220 (m110) REVERT: C 987 GLU cc_start: 0.6817 (tp30) cc_final: 0.6533 (tp30) REVERT: D 461 ASN cc_start: 0.7057 (t0) cc_final: 0.6714 (t0) REVERT: D 635 SER cc_start: 0.8349 (t) cc_final: 0.7890 (p) REVERT: D 695 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6355 (mptt) REVERT: D 770 LYS cc_start: 0.7901 (mmtp) cc_final: 0.7642 (tttp) REVERT: E 148 TYR cc_start: 0.8360 (t80) cc_final: 0.8063 (t80) REVERT: F 98 LEU cc_start: 0.7868 (tp) cc_final: 0.7644 (tt) outliers start: 69 outliers final: 55 residues processed: 331 average time/residue: 0.3002 time to fit residues: 154.5195 Evaluate side-chains 339 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 277 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 107 optimal weight: 0.0370 chunk 20 optimal weight: 0.9980 chunk 171 optimal weight: 0.3980 chunk 198 optimal weight: 0.3980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20308 Z= 0.190 Angle : 1.223 32.760 27264 Z= 0.467 Chirality : 0.141 2.210 2961 Planarity : 0.004 0.039 3162 Dihedral : 25.278 179.617 4619 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.79 % Favored : 92.86 % Rotamer: Outliers : 3.45 % Allowed : 13.76 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 2240 helix: 1.77 (0.15), residues: 1318 sheet: -2.32 (0.34), residues: 190 loop : -2.56 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 766 HIS 0.015 0.002 HIS C 412 PHE 0.020 0.001 PHE B 438 TYR 0.022 0.001 TYR E 155 ARG 0.008 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 293 time to evaluate : 2.002 Fit side-chains REVERT: A 511 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8058 (tptp) REVERT: A 585 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8034 (mmt) REVERT: A 587 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.6466 (mm-40) REVERT: A 647 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: A 663 LYS cc_start: 0.8816 (mptp) cc_final: 0.8483 (mttt) REVERT: A 669 LYS cc_start: 0.7673 (ttmt) cc_final: 0.7043 (mtpt) REVERT: A 697 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8079 (pttp) REVERT: A 952 ARG cc_start: 0.6957 (ptp-170) cc_final: 0.6612 (ptp-170) REVERT: A 985 ASN cc_start: 0.7587 (m-40) cc_final: 0.7337 (m110) REVERT: B 461 ASN cc_start: 0.7001 (t0) cc_final: 0.6757 (t0) REVERT: B 635 SER cc_start: 0.8382 (t) cc_final: 0.7912 (p) REVERT: B 695 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.6660 (mptt) REVERT: B 721 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7965 (ttp) REVERT: B 764 ASN cc_start: 0.8213 (m110) cc_final: 0.7692 (m-40) REVERT: C 503 MET cc_start: 0.8897 (ttp) cc_final: 0.8637 (ttm) REVERT: C 585 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7669 (mmt) REVERT: C 663 LYS cc_start: 0.8846 (mttp) cc_final: 0.8444 (mttt) REVERT: C 669 LYS cc_start: 0.7726 (ttmt) cc_final: 0.7153 (mtpt) REVERT: C 860 TYR cc_start: 0.8169 (m-80) cc_final: 0.7703 (m-80) REVERT: C 879 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8359 (mtpt) REVERT: C 880 MET cc_start: 0.7584 (tpp) cc_final: 0.7327 (tpp) REVERT: C 901 PHE cc_start: 0.7205 (m-10) cc_final: 0.6868 (m-10) REVERT: C 952 ARG cc_start: 0.6992 (ptp-170) cc_final: 0.6689 (ptp-170) REVERT: C 985 ASN cc_start: 0.7473 (m-40) cc_final: 0.7156 (m110) REVERT: D 461 ASN cc_start: 0.7032 (t0) cc_final: 0.6744 (t0) REVERT: D 635 SER cc_start: 0.8248 (t) cc_final: 0.7811 (p) REVERT: D 695 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6348 (mptt) REVERT: D 705 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6759 (tt0) REVERT: D 770 LYS cc_start: 0.7900 (mmtp) cc_final: 0.7674 (tttp) REVERT: F 98 LEU cc_start: 0.7816 (tp) cc_final: 0.7571 (tt) outliers start: 67 outliers final: 44 residues processed: 335 average time/residue: 0.2967 time to fit residues: 155.6691 Evaluate side-chains 330 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 277 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 191 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS C 764 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20308 Z= 0.306 Angle : 1.251 33.006 27264 Z= 0.484 Chirality : 0.141 2.226 2961 Planarity : 0.004 0.061 3162 Dihedral : 25.261 179.925 4619 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.10 % Favored : 92.59 % Rotamer: Outliers : 3.30 % Allowed : 13.87 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -0.00 (0.18), residues: 2240 helix: 1.67 (0.14), residues: 1314 sheet: -2.34 (0.33), residues: 190 loop : -2.54 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 766 HIS 0.010 0.002 HIS A 412 PHE 0.021 0.002 PHE B 438 TYR 0.028 0.002 TYR A 980 ARG 0.008 0.000 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 286 time to evaluate : 1.977 Fit side-chains REVERT: A 585 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8096 (mmt) REVERT: A 587 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.6555 (mm-40) REVERT: A 647 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7498 (m-10) REVERT: A 663 LYS cc_start: 0.8815 (mptp) cc_final: 0.8518 (mttt) REVERT: A 669 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7078 (mtpt) REVERT: A 860 TYR cc_start: 0.8099 (m-80) cc_final: 0.7746 (m-80) REVERT: A 952 ARG cc_start: 0.6983 (ptp-170) cc_final: 0.6631 (ptp-170) REVERT: A 985 ASN cc_start: 0.7590 (m-40) cc_final: 0.7304 (m110) REVERT: B 461 ASN cc_start: 0.7014 (t0) cc_final: 0.6790 (t0) REVERT: B 635 SER cc_start: 0.8425 (t) cc_final: 0.7996 (p) REVERT: B 695 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.6853 (mptt) REVERT: B 721 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.8025 (ttp) REVERT: B 764 ASN cc_start: 0.8205 (m110) cc_final: 0.7740 (m-40) REVERT: C 585 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7753 (mmt) REVERT: C 663 LYS cc_start: 0.8846 (mttp) cc_final: 0.8446 (mttt) REVERT: C 669 LYS cc_start: 0.7776 (ttmt) cc_final: 0.7131 (mtpt) REVERT: C 860 TYR cc_start: 0.8166 (m-80) cc_final: 0.7749 (m-80) REVERT: C 879 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8274 (mtpt) REVERT: C 901 PHE cc_start: 0.7233 (m-10) cc_final: 0.6885 (m-10) REVERT: C 952 ARG cc_start: 0.6991 (ptp-170) cc_final: 0.6659 (ptp-170) REVERT: D 461 ASN cc_start: 0.7056 (t0) cc_final: 0.6784 (t0) REVERT: D 635 SER cc_start: 0.8322 (t) cc_final: 0.7870 (p) REVERT: D 695 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6547 (mptt) REVERT: D 705 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6732 (tt0) REVERT: D 770 LYS cc_start: 0.7923 (mmtp) cc_final: 0.7651 (tttp) REVERT: E 148 TYR cc_start: 0.8337 (t80) cc_final: 0.7989 (t80) outliers start: 64 outliers final: 50 residues processed: 326 average time/residue: 0.3048 time to fit residues: 154.1355 Evaluate side-chains 334 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 276 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 179 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 142 optimal weight: 5.9990 chunk 190 optimal weight: 0.0470 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20308 Z= 0.208 Angle : 1.233 32.920 27264 Z= 0.473 Chirality : 0.141 2.216 2961 Planarity : 0.004 0.056 3162 Dihedral : 25.127 179.637 4619 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.19 % Favored : 92.50 % Rotamer: Outliers : 3.04 % Allowed : 14.23 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 0.14 (0.18), residues: 2240 helix: 1.78 (0.14), residues: 1312 sheet: -2.22 (0.34), residues: 190 loop : -2.48 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 766 HIS 0.014 0.002 HIS C 412 PHE 0.021 0.001 PHE B 438 TYR 0.026 0.001 TYR A 980 ARG 0.008 0.000 ARG A 684 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 276 time to evaluate : 1.997 Fit side-chains revert: symmetry clash REVERT: A 585 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8018 (mmt) REVERT: A 587 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.6418 (mm-40) REVERT: A 647 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: A 663 LYS cc_start: 0.8814 (mptp) cc_final: 0.8495 (mttt) REVERT: A 669 LYS cc_start: 0.7693 (ttmt) cc_final: 0.7070 (mtpt) REVERT: A 952 ARG cc_start: 0.6993 (ptp-170) cc_final: 0.6644 (ptp-170) REVERT: A 985 ASN cc_start: 0.7560 (m-40) cc_final: 0.7307 (m110) REVERT: B 635 SER cc_start: 0.8338 (t) cc_final: 0.7915 (p) REVERT: B 695 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.6802 (mptt) REVERT: B 721 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.8012 (ttp) REVERT: B 764 ASN cc_start: 0.8195 (m110) cc_final: 0.7723 (m-40) REVERT: C 585 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7705 (mmt) REVERT: C 663 LYS cc_start: 0.8848 (mttp) cc_final: 0.8444 (mttt) REVERT: C 669 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7154 (mtpt) REVERT: C 860 TYR cc_start: 0.8152 (m-80) cc_final: 0.7733 (m-80) REVERT: C 879 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8208 (mtpt) REVERT: C 901 PHE cc_start: 0.7216 (m-10) cc_final: 0.6908 (m-10) REVERT: C 952 ARG cc_start: 0.6990 (ptp-170) cc_final: 0.6647 (ptp-170) REVERT: D 461 ASN cc_start: 0.7013 (t0) cc_final: 0.6753 (t0) REVERT: D 635 SER cc_start: 0.8220 (t) cc_final: 0.7813 (p) REVERT: D 695 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6485 (mptt) REVERT: D 705 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6570 (tt0) REVERT: D 770 LYS cc_start: 0.7892 (mmtp) cc_final: 0.7640 (tttp) REVERT: F 98 LEU cc_start: 0.7826 (tp) cc_final: 0.7560 (tt) outliers start: 59 outliers final: 44 residues processed: 313 average time/residue: 0.3075 time to fit residues: 148.9870 Evaluate side-chains 325 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 273 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 0.0050 chunk 165 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 179 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 184 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.173583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126277 restraints weight = 22083.600| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.00 r_work: 0.3089 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20308 Z= 0.185 Angle : 1.224 32.736 27264 Z= 0.468 Chirality : 0.141 2.198 2961 Planarity : 0.004 0.053 3162 Dihedral : 24.965 179.297 4619 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.92 % Favored : 92.81 % Rotamer: Outliers : 2.84 % Allowed : 14.28 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 0.29 (0.18), residues: 2240 helix: 1.90 (0.15), residues: 1312 sheet: -2.07 (0.34), residues: 190 loop : -2.44 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 766 HIS 0.019 0.002 HIS A 412 PHE 0.020 0.001 PHE B 438 TYR 0.026 0.001 TYR A 980 ARG 0.008 0.000 ARG A 684 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4758.20 seconds wall clock time: 88 minutes 31.33 seconds (5311.33 seconds total)