Starting phenix.real_space_refine on Tue Mar 19 15:18:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eos_31229/03_2024/7eos_31229.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eos_31229/03_2024/7eos_31229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eos_31229/03_2024/7eos_31229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eos_31229/03_2024/7eos_31229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eos_31229/03_2024/7eos_31229.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eos_31229/03_2024/7eos_31229.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 15760 2.51 5 N 4120 2.21 5 O 4570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24600 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6007 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 29, 'TRANS': 734} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 6167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6167 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 6007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6007 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 29, 'TRANS': 734} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 6167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6167 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 13.21, per 1000 atoms: 0.54 Number of scatterers: 24600 At special positions: 0 Unit cell: (120.91, 148.73, 188.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 4570 8.00 N 4120 7.00 C 15760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS A 745 " - pdb=" SG CYS A 800 " distance=2.03 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS D 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 79 " - pdb=" SG CYS B 308 " distance=2.04 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS C 794 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 456 " distance=2.03 Simple disulfide: pdb=" SG CYS C 745 " - pdb=" SG CYS C 800 " distance=2.03 Simple disulfide: pdb=" SG CYS D 79 " - pdb=" SG CYS D 308 " distance=2.04 Simple disulfide: pdb=" SG CYS D 420 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 744 " - pdb=" SG CYS D 798 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 340 " " NAG A 902 " - " ASN A 687 " " NAG B 901 " - " ASN B 61 " " NAG B 902 " - " ASN B 276 " " NAG B 903 " - " ASN B 368 " " NAG B 904 " - " ASN B 471 " " NAG B 905 " - " ASN B 771 " " NAG B 906 " - " ASN B 203 " " NAG B 907 " - " ASN B 239 " " NAG C 901 " - " ASN C 340 " " NAG C 902 " - " ASN C 687 " " NAG D 901 " - " ASN D 61 " " NAG D 902 " - " ASN D 276 " " NAG D 903 " - " ASN D 368 " " NAG D 904 " - " ASN D 471 " " NAG D 905 " - " ASN D 771 " " NAG D 906 " - " ASN D 203 " " NAG D 907 " - " ASN D 239 " Time building additional restraints: 9.81 Conformation dependent library (CDL) restraints added in 4.7 seconds 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5808 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 24 sheets defined 42.9% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.657A pdb=" N ARG A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 106 through 121 removed outlier: 4.473A pdb=" N ALA A 110 " --> pdb=" O GLN A 106 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 116 " --> pdb=" O MET A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 166 Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 232 through 247 removed outlier: 3.773A pdb=" N VAL A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 310 Processing helix chain 'A' and resid 459 through 472 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 515 through 522 removed outlier: 4.130A pdb=" N GLU A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 579 removed outlier: 4.057A pdb=" N VAL A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.791A pdb=" N TRP A 609 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A 611 " --> pdb=" O LEU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 653 Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.817A pdb=" N GLN A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 removed outlier: 3.739A pdb=" N TYR A 676 " --> pdb=" O PRO A 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 676' Processing helix chain 'A' and resid 689 through 698 Processing helix chain 'A' and resid 698 through 708 removed outlier: 3.906A pdb=" N LYS A 707 " --> pdb=" O GLN A 703 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 770 through 786 removed outlier: 4.596A pdb=" N GLN A 774 " --> pdb=" O PRO A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 Processing helix chain 'A' and resid 814 through 837 removed outlier: 4.131A pdb=" N ALA A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 825 " --> pdb=" O PHE A 821 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 52 Processing helix chain 'B' and resid 70 through 83 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 104 through 112 removed outlier: 3.675A pdb=" N SER B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 159 removed outlier: 4.098A pdb=" N VAL B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 224 through 238 Processing helix chain 'B' and resid 256 through 262 removed outlier: 4.251A pdb=" N ARG B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 296 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 381 through 385 removed outlier: 4.022A pdb=" N GLU B 385 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.894A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 560 through 584 Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'B' and resid 627 through 657 removed outlier: 3.614A pdb=" N ILE B 631 " --> pdb=" O PHE B 627 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 Processing helix chain 'B' and resid 700 through 707 removed outlier: 4.059A pdb=" N ARG B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 768 through 782 removed outlier: 3.986A pdb=" N SER B 775 " --> pdb=" O ASN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 removed outlier: 3.792A pdb=" N ARG B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 843 removed outlier: 3.559A pdb=" N HIS B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 56 removed outlier: 3.533A pdb=" N ARG C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.616A pdb=" N GLN C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 116 " --> pdb=" O MET C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 166 Processing helix chain 'C' and resid 179 through 192 Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 232 through 247 removed outlier: 3.817A pdb=" N VAL C 237 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 310 Processing helix chain 'C' and resid 459 through 472 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'C' and resid 515 through 522 removed outlier: 4.115A pdb=" N GLU C 520 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C 521 " --> pdb=" O GLU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 579 removed outlier: 4.034A pdb=" N VAL C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 563 " --> pdb=" O VAL C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.784A pdb=" N TRP C 609 " --> pdb=" O ILE C 605 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU C 611 " --> pdb=" O LEU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 652 Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.806A pdb=" N GLN C 671 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 676 removed outlier: 3.730A pdb=" N TYR C 676 " --> pdb=" O PRO C 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 673 through 676' Processing helix chain 'C' and resid 688 through 698 removed outlier: 4.004A pdb=" N ARG C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 708 removed outlier: 3.902A pdb=" N LYS C 707 " --> pdb=" O GLN C 703 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 722 Processing helix chain 'C' and resid 732 through 741 Processing helix chain 'C' and resid 770 through 786 removed outlier: 4.570A pdb=" N GLN C 774 " --> pdb=" O PRO C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 796 Processing helix chain 'C' and resid 814 through 837 removed outlier: 4.142A pdb=" N ALA C 818 " --> pdb=" O ILE C 814 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET C 823 " --> pdb=" O GLY C 819 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 824 " --> pdb=" O VAL C 820 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 825 " --> pdb=" O PHE C 821 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 52 Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.653A pdb=" N SER D 108 " --> pdb=" O PRO D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 146 through 159 removed outlier: 4.078A pdb=" N VAL D 150 " --> pdb=" O HIS D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 224 through 238 Processing helix chain 'D' and resid 256 through 262 removed outlier: 4.260A pdb=" N ARG D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 296 Processing helix chain 'D' and resid 317 through 327 Processing helix chain 'D' and resid 381 through 385 removed outlier: 4.028A pdb=" N GLU D 385 " --> pdb=" O PRO D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.901A pdb=" N LEU D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 560 through 584 Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 627 through 657 removed outlier: 3.677A pdb=" N ILE D 631 " --> pdb=" O PHE D 627 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU D 632 " --> pdb=" O SER D 628 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET D 641 " --> pdb=" O ALA D 637 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE D 643 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 695 Processing helix chain 'D' and resid 700 through 707 removed outlier: 4.048A pdb=" N ARG D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 768 through 782 removed outlier: 3.988A pdb=" N SER D 775 " --> pdb=" O ASN D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 794 removed outlier: 3.784A pdb=" N ARG D 794 " --> pdb=" O LYS D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 843 removed outlier: 3.566A pdb=" N HIS D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 73 removed outlier: 6.738A pdb=" N ASN A 35 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL A 99 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 37 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 125 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 100 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 124 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 205 removed outlier: 6.259A pdb=" N LEU A 172 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 256 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 229 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 279 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A 373 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 478 through 479 removed outlier: 3.927A pdb=" N ASP A 523 " --> pdb=" O LEU A 765 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 417 through 420 removed outlier: 3.818A pdb=" N CYS A 455 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 450 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 440 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 438 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AA6, first strand: chain 'A' and resid 682 through 683 removed outlier: 6.374A pdb=" N GLY A 683 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N ASP A 731 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 537 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL A 748 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 63 through 66 removed outlier: 7.057A pdb=" N ILE B 90 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 194 through 197 removed outlier: 6.527A pdb=" N LEU B 165 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE B 197 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL B 167 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 164 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 220 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 168 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 267 through 271 removed outlier: 4.286A pdb=" N GLY B 365 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN B 355 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLN B 363 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN B 357 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU B 361 " --> pdb=" O GLN B 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 397 through 402 removed outlier: 3.675A pdb=" N LEU B 398 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU B 475 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE B 435 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N LEU B 478 " --> pdb=" O ILE B 435 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N THR B 437 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 434 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS B 455 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 487 through 488 removed outlier: 4.558A pdb=" N GLU B 497 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 681 through 682 removed outlier: 3.999A pdb=" N ALA B 682 " --> pdb=" O ALA B 728 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE B 730 " --> pdb=" O ALA B 682 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP B 731 " --> pdb=" O THR B 539 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N GLN B 536 " --> pdb=" O PHE B 753 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE B 753 " --> pdb=" O GLN B 536 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 538 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU B 751 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 540 " --> pdb=" O THR B 749 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 747 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 68 through 72 removed outlier: 6.696A pdb=" N ASN C 35 " --> pdb=" O GLY C 97 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL C 99 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA C 37 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 125 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE C 100 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 124 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 204 through 205 removed outlier: 6.250A pdb=" N LEU C 172 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 256 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 229 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 279 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 373 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 478 through 479 removed outlier: 3.930A pdb=" N ASP C 523 " --> pdb=" O LEU C 765 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 417 through 420 removed outlier: 3.817A pdb=" N CYS C 455 " --> pdb=" O GLU C 420 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET C 450 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 440 " --> pdb=" O MET C 450 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 438 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 530 through 531 Processing sheet with id=AB9, first strand: chain 'C' and resid 682 through 683 removed outlier: 6.371A pdb=" N GLY C 683 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ASP C 731 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL C 537 " --> pdb=" O VAL C 748 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 748 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 61 through 66 removed outlier: 3.937A pdb=" N ILE D 29 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE D 90 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 194 through 197 removed outlier: 6.562A pdb=" N LEU D 165 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE D 197 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL D 167 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 164 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 220 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER D 168 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 267 through 271 removed outlier: 4.299A pdb=" N GLY D 365 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN D 355 " --> pdb=" O GLN D 363 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLN D 363 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN D 357 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU D 361 " --> pdb=" O GLN D 357 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 397 through 402 removed outlier: 3.691A pdb=" N LEU D 398 " --> pdb=" O THR D 473 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU D 475 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE D 435 " --> pdb=" O VAL D 476 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N LEU D 478 " --> pdb=" O ILE D 435 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N THR D 437 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 487 through 488 removed outlier: 4.500A pdb=" N GLU D 497 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 681 through 682 removed outlier: 3.997A pdb=" N ALA D 682 " --> pdb=" O ALA D 728 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE D 730 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP D 731 " --> pdb=" O THR D 539 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLN D 536 " --> pdb=" O PHE D 753 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE D 753 " --> pdb=" O GLN D 536 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU D 538 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLU D 751 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE D 540 " --> pdb=" O THR D 749 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 747 " --> pdb=" O VAL D 542 " (cutoff:3.500A) 982 hydrogen bonds defined for protein. 2892 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: 8.10 Time building geometry restraints manager: 10.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7858 1.34 - 1.46: 5880 1.46 - 1.58: 11160 1.58 - 1.70: 0 1.70 - 1.81: 256 Bond restraints: 25154 Sorted by residual: bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C1 NAG D 901 " pdb=" O5 NAG D 901 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 NAG C 901 " pdb=" O5 NAG C 901 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C1 NAG B 904 " pdb=" O5 NAG B 904 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.42e+00 ... (remaining 25149 not shown) Histogram of bond angle deviations from ideal: 100.57 - 107.26: 887 107.26 - 113.96: 14337 113.96 - 120.66: 9927 120.66 - 127.36: 8669 127.36 - 134.05: 292 Bond angle restraints: 34112 Sorted by residual: angle pdb=" C MET D 394 " pdb=" N SER D 395 " pdb=" CA SER D 395 " ideal model delta sigma weight residual 121.54 126.42 -4.88 1.91e+00 2.74e-01 6.53e+00 angle pdb=" C MET B 394 " pdb=" N SER B 395 " pdb=" CA SER B 395 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.46e+00 angle pdb=" C GLY C 41 " pdb=" N HIS C 42 " pdb=" CA HIS C 42 " ideal model delta sigma weight residual 122.46 125.22 -2.76 1.41e+00 5.03e-01 3.82e+00 angle pdb=" CA LEU C 89 " pdb=" CB LEU C 89 " pdb=" CG LEU C 89 " ideal model delta sigma weight residual 116.30 123.12 -6.82 3.50e+00 8.16e-02 3.80e+00 angle pdb=" N GLN C 661 " pdb=" CA GLN C 661 " pdb=" C GLN C 661 " ideal model delta sigma weight residual 112.93 110.34 2.59 1.33e+00 5.65e-01 3.80e+00 ... (remaining 34107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.93: 14756 22.93 - 45.86: 386 45.86 - 68.79: 39 68.79 - 91.72: 1 91.72 - 114.65: 6 Dihedral angle restraints: 15188 sinusoidal: 6194 harmonic: 8994 Sorted by residual: dihedral pdb=" C1 NAG B 901 " pdb=" C5 NAG B 901 " pdb=" O5 NAG B 901 " pdb=" C4 NAG B 901 " ideal model delta sinusoidal sigma weight residual -64.11 50.54 -114.65 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C1 NAG D 901 " pdb=" C5 NAG D 901 " pdb=" O5 NAG D 901 " pdb=" C6 NAG D 901 " ideal model delta sinusoidal sigma weight residual 171.16 -74.25 -114.59 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C1 NAG D 901 " pdb=" C5 NAG D 901 " pdb=" O5 NAG D 901 " pdb=" C4 NAG D 901 " ideal model delta sinusoidal sigma weight residual -64.11 50.47 -114.58 1 3.00e+01 1.11e-03 1.51e+01 ... (remaining 15185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3302 0.055 - 0.109: 533 0.109 - 0.164: 69 0.164 - 0.219: 0 0.219 - 0.274: 2 Chirality restraints: 3906 Sorted by residual: chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 340 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG C 901 " pdb=" ND2 ASN C 340 " pdb=" C2 NAG C 901 " pdb=" O5 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C1 NAG D 901 " pdb=" ND2 ASN D 61 " pdb=" C2 NAG D 901 " pdb=" O5 NAG D 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 3903 not shown) Planarity restraints: 4314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 390 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 391 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 391 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 391 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 390 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO C 391 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 391 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 391 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 139 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 140 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " -0.015 5.00e-02 4.00e+02 ... (remaining 4311 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5191 2.78 - 3.31: 24365 3.31 - 3.84: 39025 3.84 - 4.37: 42673 4.37 - 4.90: 74695 Nonbonded interactions: 185949 Sorted by model distance: nonbonded pdb=" O THR D 396 " pdb=" OG1 THR D 473 " model vdw 2.254 2.440 nonbonded pdb=" O THR B 396 " pdb=" OG1 THR B 473 " model vdw 2.263 2.440 nonbonded pdb=" O GLU D 80 " pdb=" OG SER D 84 " model vdw 2.270 2.440 nonbonded pdb=" O GLU B 80 " pdb=" OG SER B 84 " model vdw 2.278 2.440 nonbonded pdb=" O PHE C 680 " pdb=" OH TYR C 704 " model vdw 2.285 2.440 ... (remaining 185944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.160 Check model and map are aligned: 0.390 Set scattering table: 0.220 Process input model: 65.230 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 76.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 : 0.002 0.082 25154 Z= 0.136 Angle : 0.421 6.823 34112 Z= 0.207 Chirality : 0.041 0.274 3906 Planarity : 0.002 0.031 4296 Dihedral : 9.752 114.648 9326 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.14 % Favored : 95.79 % Rotamer: Outliers : 1.89 % Allowed : 6.63 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 3066 helix: 1.89 (0.15), residues: 1262 sheet: 0.46 (0.29), residues: 372 loop : -1.24 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP C 378 HIS 0.001 0.000 HIS A 485 PHE 0.008 0.001 PHE C 652 TYR 0.007 0.001 TYR C 737 ARG 0.001 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 351 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8688 (mtt) cc_final: 0.8277 (mtm) REVERT: A 183 PHE cc_start: 0.6256 (m-10) cc_final: 0.5759 (m-80) REVERT: A 331 MET cc_start: 0.4303 (ttt) cc_final: 0.2919 (tpp) REVERT: A 389 VAL cc_start: 0.6563 (OUTLIER) cc_final: 0.6173 (t) REVERT: A 396 PHE cc_start: 0.5997 (m-80) cc_final: 0.5767 (m-80) REVERT: A 817 MET cc_start: 0.4901 (mpp) cc_final: 0.4205 (ptt) REVERT: B 343 ASP cc_start: 0.8489 (m-30) cc_final: 0.8190 (p0) REVERT: B 639 PHE cc_start: 0.8312 (t80) cc_final: 0.7917 (t80) REVERT: B 706 MET cc_start: 0.8462 (mtm) cc_final: 0.8014 (mtp) REVERT: B 813 MET cc_start: 0.7733 (mpp) cc_final: 0.7495 (ppp) REVERT: C 158 MET cc_start: 0.8692 (mtt) cc_final: 0.8301 (mtm) REVERT: C 320 CYS cc_start: 0.4525 (OUTLIER) cc_final: 0.3946 (p) REVERT: C 331 MET cc_start: 0.3982 (ttt) cc_final: 0.2655 (tpp) REVERT: C 380 ASN cc_start: 0.7490 (p0) cc_final: 0.7235 (p0) REVERT: C 389 VAL cc_start: 0.6552 (OUTLIER) cc_final: 0.6070 (t) REVERT: C 396 PHE cc_start: 0.6139 (m-80) cc_final: 0.5835 (m-80) REVERT: C 637 PHE cc_start: 0.8642 (t80) cc_final: 0.8092 (m-10) REVERT: C 817 MET cc_start: 0.4881 (mpp) cc_final: 0.4338 (ptt) REVERT: C 828 MET cc_start: 0.8604 (tpp) cc_final: 0.8279 (mtt) REVERT: D 237 MET cc_start: 0.8884 (tmm) cc_final: 0.8667 (tmm) REVERT: D 343 ASP cc_start: 0.8476 (m-30) cc_final: 0.8145 (p0) REVERT: D 762 MET cc_start: 0.8224 (mtm) cc_final: 0.7850 (mtp) outliers start: 50 outliers final: 15 residues processed: 398 average time/residue: 0.3744 time to fit residues: 232.7076 Evaluate side-chains 232 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 214 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 367 ASN B 477 HIS ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 GLN D 477 HIS D 696 GLN D 710 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 25154 Z= 0.443 Angle : 0.754 14.196 34112 Z= 0.385 Chirality : 0.046 0.278 3906 Planarity : 0.005 0.043 4296 Dihedral : 7.266 87.079 3714 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 3.07 % Allowed : 10.61 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 3066 helix: 1.58 (0.15), residues: 1256 sheet: -0.36 (0.26), residues: 452 loop : -1.35 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 55 HIS 0.008 0.001 HIS D 171 PHE 0.035 0.003 PHE B 533 TYR 0.023 0.002 TYR C 180 ARG 0.006 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 181 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 800 CYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7364 (m) REVERT: A 817 MET cc_start: 0.5312 (mpp) cc_final: 0.4517 (ptt) REVERT: B 237 MET cc_start: 0.8821 (tmm) cc_final: 0.8557 (ppp) REVERT: B 354 MET cc_start: 0.8285 (tpp) cc_final: 0.7975 (tpp) REVERT: B 706 MET cc_start: 0.8783 (mtm) cc_final: 0.8578 (mtp) REVERT: B 813 MET cc_start: 0.7676 (mpp) cc_final: 0.7399 (tmm) REVERT: C 320 CYS cc_start: 0.4796 (OUTLIER) cc_final: 0.4267 (p) REVERT: C 473 PHE cc_start: 0.6972 (m-80) cc_final: 0.6191 (m-80) REVERT: C 637 PHE cc_start: 0.8737 (t80) cc_final: 0.8143 (m-80) REVERT: C 817 MET cc_start: 0.5046 (mpp) cc_final: 0.4571 (mtm) REVERT: C 823 MET cc_start: 0.8420 (ppp) cc_final: 0.8157 (ppp) REVERT: C 828 MET cc_start: 0.8594 (tpp) cc_final: 0.8227 (mtt) REVERT: D 354 MET cc_start: 0.8272 (tpp) cc_final: 0.8013 (tpp) outliers start: 81 outliers final: 40 residues processed: 253 average time/residue: 0.3297 time to fit residues: 136.0398 Evaluate side-chains 210 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 652 PHE Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 533 PHE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 280 optimal weight: 0.9990 chunk 302 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25154 Z= 0.199 Angle : 0.548 11.230 34112 Z= 0.274 Chirality : 0.043 0.277 3906 Planarity : 0.003 0.039 4296 Dihedral : 6.090 74.677 3706 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.83 % Favored : 95.11 % Rotamer: Outliers : 2.50 % Allowed : 12.20 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 3066 helix: 1.65 (0.15), residues: 1254 sheet: -0.40 (0.25), residues: 458 loop : -1.35 (0.18), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 792 HIS 0.008 0.001 HIS A 119 PHE 0.028 0.001 PHE A 183 TYR 0.032 0.001 TYR B 692 ARG 0.004 0.000 ARG B 755 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 169 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 ARG cc_start: 0.5653 (ptt-90) cc_final: 0.5410 (ptt-90) REVERT: A 800 CYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7310 (m) REVERT: A 817 MET cc_start: 0.5088 (mpp) cc_final: 0.4337 (ptt) REVERT: B 354 MET cc_start: 0.8400 (tpp) cc_final: 0.7985 (tpp) REVERT: B 611 TRP cc_start: 0.5177 (m100) cc_final: 0.4947 (m100) REVERT: B 616 ASN cc_start: 0.7209 (OUTLIER) cc_final: 0.6801 (t0) REVERT: B 813 MET cc_start: 0.7704 (mpp) cc_final: 0.7413 (tmm) REVERT: C 320 CYS cc_start: 0.4697 (OUTLIER) cc_final: 0.4146 (p) REVERT: C 392 ARG cc_start: 0.5569 (ptt-90) cc_final: 0.5314 (ptt-90) REVERT: C 637 PHE cc_start: 0.8662 (t80) cc_final: 0.8071 (m-80) REVERT: C 817 MET cc_start: 0.4993 (mpp) cc_final: 0.4647 (mtm) REVERT: C 828 MET cc_start: 0.8607 (tpp) cc_final: 0.8262 (mtt) REVERT: D 28 ASN cc_start: 0.4785 (OUTLIER) cc_final: 0.2929 (t0) REVERT: D 354 MET cc_start: 0.8301 (tpp) cc_final: 0.7963 (tpp) outliers start: 66 outliers final: 33 residues processed: 229 average time/residue: 0.3279 time to fit residues: 122.7765 Evaluate side-chains 197 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 TRP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 533 PHE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 10.0000 chunk 210 optimal weight: 50.0000 chunk 145 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 133 optimal weight: 30.0000 chunk 188 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 266 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25154 Z= 0.221 Angle : 0.556 12.123 34112 Z= 0.280 Chirality : 0.043 0.280 3906 Planarity : 0.003 0.037 4296 Dihedral : 5.204 59.919 3706 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.87 % Favored : 94.06 % Rotamer: Outliers : 2.54 % Allowed : 13.07 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 3066 helix: 1.58 (0.15), residues: 1256 sheet: -0.56 (0.25), residues: 466 loop : -1.38 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 151 HIS 0.006 0.001 HIS A 119 PHE 0.052 0.002 PHE A 183 TYR 0.023 0.001 TYR D 692 ARG 0.004 0.000 ARG B 755 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 164 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7409 (p90) REVERT: A 817 MET cc_start: 0.5275 (mpp) cc_final: 0.4482 (mtm) REVERT: B 354 MET cc_start: 0.8400 (tpp) cc_final: 0.7943 (tpp) REVERT: B 813 MET cc_start: 0.7711 (mpp) cc_final: 0.7399 (tmm) REVERT: C 200 MET cc_start: 0.7089 (tpp) cc_final: 0.6608 (tpp) REVERT: C 320 CYS cc_start: 0.4542 (OUTLIER) cc_final: 0.4026 (p) REVERT: C 637 PHE cc_start: 0.8676 (t80) cc_final: 0.8084 (m-80) REVERT: C 817 MET cc_start: 0.4894 (mpp) cc_final: 0.4618 (mtm) REVERT: C 828 MET cc_start: 0.8620 (tpp) cc_final: 0.8301 (mtt) REVERT: D 74 MET cc_start: 0.6848 (ppp) cc_final: 0.6641 (ppp) REVERT: D 354 MET cc_start: 0.8333 (tpp) cc_final: 0.7967 (tpp) outliers start: 67 outliers final: 49 residues processed: 223 average time/residue: 0.3322 time to fit residues: 120.9370 Evaluate side-chains 210 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 159 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 198 TRP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 533 PHE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 8.9990 chunk 168 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 205 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 50.0000 chunk 267 optimal weight: 0.9990 chunk 75 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 367 ASN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 710 ASN ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25154 Z= 0.329 Angle : 0.637 11.164 34112 Z= 0.329 Chirality : 0.044 0.279 3906 Planarity : 0.004 0.042 4296 Dihedral : 5.481 58.907 3706 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.95 % Favored : 92.99 % Rotamer: Outliers : 3.60 % Allowed : 13.14 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 3066 helix: 1.29 (0.15), residues: 1268 sheet: -0.70 (0.26), residues: 444 loop : -1.58 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 315 HIS 0.006 0.001 HIS C 332 PHE 0.054 0.002 PHE A 183 TYR 0.035 0.002 TYR B 692 ARG 0.006 0.001 ARG D 695 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 164 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 PHE cc_start: 0.6915 (m-80) cc_final: 0.6318 (m-80) REVERT: A 524 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7717 (p90) REVERT: A 800 CYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7755 (m) REVERT: A 817 MET cc_start: 0.5539 (mpp) cc_final: 0.4737 (mtm) REVERT: B 74 MET cc_start: 0.7124 (ppp) cc_final: 0.6786 (ppp) REVERT: B 354 MET cc_start: 0.8320 (tpp) cc_final: 0.7852 (tpp) REVERT: B 611 TRP cc_start: 0.5386 (m100) cc_final: 0.5153 (m100) REVERT: B 813 MET cc_start: 0.7934 (mpp) cc_final: 0.7556 (tmm) REVERT: C 473 PHE cc_start: 0.6817 (m-80) cc_final: 0.6236 (m-80) REVERT: C 524 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7747 (p90) REVERT: C 637 PHE cc_start: 0.8686 (t80) cc_final: 0.8069 (m-80) REVERT: C 817 MET cc_start: 0.4966 (mpp) cc_final: 0.4691 (mtm) REVERT: C 828 MET cc_start: 0.8571 (tpp) cc_final: 0.8287 (mtt) REVERT: D 74 MET cc_start: 0.7153 (ppp) cc_final: 0.6930 (ppp) REVERT: D 354 MET cc_start: 0.8305 (tpp) cc_final: 0.7785 (tpp) REVERT: D 392 TYR cc_start: 0.7632 (m-10) cc_final: 0.7240 (m-10) REVERT: D 697 VAL cc_start: 0.8734 (m) cc_final: 0.8511 (p) outliers start: 95 outliers final: 66 residues processed: 248 average time/residue: 0.2994 time to fit residues: 123.6426 Evaluate side-chains 224 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 155 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 198 TRP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 494 ASN Chi-restraints excluded: chain D residue 533 PHE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 8.9990 chunk 268 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 174 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 chunk 247 optimal weight: 8.9990 chunk 137 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS B 696 GLN B 710 ASN C 201 GLN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 GLN ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 25154 Z= 0.378 Angle : 0.680 12.826 34112 Z= 0.350 Chirality : 0.045 0.275 3906 Planarity : 0.004 0.042 4296 Dihedral : 5.705 58.462 3705 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.44 % Favored : 92.50 % Rotamer: Outliers : 3.90 % Allowed : 13.83 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 3066 helix: 1.05 (0.14), residues: 1266 sheet: -0.84 (0.26), residues: 432 loop : -1.78 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 634 HIS 0.007 0.001 HIS A 332 PHE 0.048 0.002 PHE A 183 TYR 0.031 0.002 TYR B 692 ARG 0.004 0.001 ARG C 431 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 158 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 PHE cc_start: 0.6840 (m-80) cc_final: 0.6232 (m-80) REVERT: A 524 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8280 (p90) REVERT: A 789 GLU cc_start: 0.8135 (mp0) cc_final: 0.7888 (mp0) REVERT: A 817 MET cc_start: 0.5504 (mpp) cc_final: 0.4656 (mtm) REVERT: B 354 MET cc_start: 0.8255 (tpp) cc_final: 0.7787 (tpp) REVERT: B 392 TYR cc_start: 0.7706 (m-10) cc_final: 0.7424 (m-10) REVERT: B 813 MET cc_start: 0.8124 (mpp) cc_final: 0.7606 (tmm) REVERT: C 473 PHE cc_start: 0.6915 (m-80) cc_final: 0.6344 (m-80) REVERT: C 524 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8256 (p90) REVERT: C 637 PHE cc_start: 0.8711 (t80) cc_final: 0.8019 (m-80) REVERT: C 817 MET cc_start: 0.5238 (mpp) cc_final: 0.4890 (mtm) REVERT: C 828 MET cc_start: 0.8610 (tpp) cc_final: 0.8299 (mtt) REVERT: D 74 MET cc_start: 0.7699 (ppp) cc_final: 0.7460 (ppp) REVERT: D 354 MET cc_start: 0.8337 (tpp) cc_final: 0.7841 (tpp) REVERT: D 392 TYR cc_start: 0.7757 (m-10) cc_final: 0.7298 (m-10) REVERT: D 611 TRP cc_start: 0.5933 (m100) cc_final: 0.5621 (m100) REVERT: D 697 VAL cc_start: 0.8882 (m) cc_final: 0.8598 (p) outliers start: 103 outliers final: 74 residues processed: 251 average time/residue: 0.3209 time to fit residues: 133.5445 Evaluate side-chains 230 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 154 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 198 TRP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 113 PHE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 533 PHE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 217 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 chunk 250 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 296 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 137 optimal weight: 0.0870 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN C 710 GLN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 25154 Z= 0.154 Angle : 0.575 13.355 34112 Z= 0.290 Chirality : 0.043 0.287 3906 Planarity : 0.003 0.044 4296 Dihedral : 4.886 53.686 3703 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.10 % Favored : 93.84 % Rotamer: Outliers : 2.23 % Allowed : 15.72 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 3066 helix: 1.22 (0.15), residues: 1266 sheet: -0.61 (0.26), residues: 436 loop : -1.61 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 198 HIS 0.006 0.001 HIS B 67 PHE 0.046 0.001 PHE A 183 TYR 0.017 0.001 TYR D 692 ARG 0.005 0.000 ARG D 694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 167 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 PHE cc_start: 0.6649 (m-80) cc_final: 0.6063 (m-80) REVERT: A 524 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.8057 (p90) REVERT: A 609 TRP cc_start: 0.8302 (m100) cc_final: 0.8042 (m100) REVERT: A 653 MET cc_start: 0.6406 (mmm) cc_final: 0.5761 (mpp) REVERT: A 817 MET cc_start: 0.5435 (mpp) cc_final: 0.4604 (mtm) REVERT: B 74 MET cc_start: 0.7192 (ppp) cc_final: 0.6846 (ppp) REVERT: B 354 MET cc_start: 0.8290 (tpp) cc_final: 0.7831 (tpp) REVERT: B 378 LYS cc_start: 0.7395 (tmtt) cc_final: 0.6954 (tptp) REVERT: B 611 TRP cc_start: 0.5619 (m100) cc_final: 0.5345 (m100) REVERT: B 813 MET cc_start: 0.8094 (mpp) cc_final: 0.7637 (tmm) REVERT: C 473 PHE cc_start: 0.6721 (m-80) cc_final: 0.6176 (m-80) REVERT: C 524 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8002 (p90) REVERT: C 637 PHE cc_start: 0.8690 (t80) cc_final: 0.8025 (m-80) REVERT: C 789 GLU cc_start: 0.8043 (mp0) cc_final: 0.7805 (mp0) REVERT: C 817 MET cc_start: 0.5137 (mpp) cc_final: 0.4710 (mtm) REVERT: C 828 MET cc_start: 0.8673 (tpp) cc_final: 0.8387 (mtt) REVERT: D 354 MET cc_start: 0.8270 (tpp) cc_final: 0.7810 (tpp) REVERT: D 392 TYR cc_start: 0.7609 (m-10) cc_final: 0.7395 (m-10) REVERT: D 571 HIS cc_start: 0.6111 (m-70) cc_final: 0.5905 (m-70) REVERT: D 611 TRP cc_start: 0.5921 (m100) cc_final: 0.5590 (m100) REVERT: D 697 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8525 (p) outliers start: 59 outliers final: 40 residues processed: 219 average time/residue: 0.3342 time to fit residues: 119.7262 Evaluate side-chains 200 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 157 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 198 TRP Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 697 VAL Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 177 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 233 optimal weight: 30.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25154 Z= 0.313 Angle : 0.663 15.626 34112 Z= 0.334 Chirality : 0.044 0.286 3906 Planarity : 0.004 0.037 4296 Dihedral : 5.143 50.105 3703 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.24 % Favored : 92.69 % Rotamer: Outliers : 2.65 % Allowed : 16.33 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 3066 helix: 1.13 (0.15), residues: 1280 sheet: -0.80 (0.26), residues: 442 loop : -1.77 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 151 HIS 0.006 0.001 HIS B 67 PHE 0.056 0.002 PHE A 183 TYR 0.024 0.002 TYR D 692 ARG 0.009 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 155 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 MET cc_start: 0.4675 (pmm) cc_final: 0.3778 (pmm) REVERT: A 473 PHE cc_start: 0.6866 (m-80) cc_final: 0.6294 (m-80) REVERT: A 524 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8208 (p90) REVERT: A 609 TRP cc_start: 0.8349 (m100) cc_final: 0.8096 (m100) REVERT: A 789 GLU cc_start: 0.8153 (mp0) cc_final: 0.7864 (mp0) REVERT: A 817 MET cc_start: 0.5514 (mpp) cc_final: 0.4640 (mtm) REVERT: B 28 ASN cc_start: 0.5821 (OUTLIER) cc_final: 0.4428 (t0) REVERT: B 74 MET cc_start: 0.7319 (ppp) cc_final: 0.6929 (ppp) REVERT: B 354 MET cc_start: 0.8245 (tpp) cc_final: 0.7809 (tpp) REVERT: B 392 TYR cc_start: 0.7694 (m-10) cc_final: 0.7326 (m-10) REVERT: B 611 TRP cc_start: 0.5941 (m100) cc_final: 0.5645 (m100) REVERT: B 692 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6520 (t80) REVERT: B 813 MET cc_start: 0.8002 (mpp) cc_final: 0.7570 (tmm) REVERT: C 220 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8039 (mmtm) REVERT: C 473 PHE cc_start: 0.6889 (m-80) cc_final: 0.6333 (m-80) REVERT: C 524 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8117 (p90) REVERT: C 637 PHE cc_start: 0.8753 (t80) cc_final: 0.8087 (m-80) REVERT: C 817 MET cc_start: 0.5215 (mpp) cc_final: 0.4877 (mtm) REVERT: C 828 MET cc_start: 0.8687 (tpp) cc_final: 0.8391 (mtt) REVERT: D 354 MET cc_start: 0.8298 (tpp) cc_final: 0.7840 (tpp) REVERT: D 392 TYR cc_start: 0.7767 (m-10) cc_final: 0.7443 (m-10) REVERT: D 611 TRP cc_start: 0.6120 (m100) cc_final: 0.5773 (m100) REVERT: D 697 VAL cc_start: 0.8970 (m) cc_final: 0.8651 (p) outliers start: 70 outliers final: 50 residues processed: 216 average time/residue: 0.3323 time to fit residues: 118.4321 Evaluate side-chains 207 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 153 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 198 TRP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 692 TYR Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 113 PHE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 533 PHE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 chunk 259 optimal weight: 0.9980 chunk 276 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 261 optimal weight: 0.0000 chunk 275 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25154 Z= 0.163 Angle : 0.611 14.105 34112 Z= 0.302 Chirality : 0.043 0.288 3906 Planarity : 0.003 0.044 4296 Dihedral : 4.838 50.848 3703 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.03 % Rotamer: Outliers : 1.97 % Allowed : 17.12 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 3066 helix: 1.14 (0.15), residues: 1282 sheet: -0.52 (0.26), residues: 428 loop : -1.70 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 611 HIS 0.006 0.001 HIS C 119 PHE 0.052 0.001 PHE A 183 TYR 0.029 0.001 TYR B 692 ARG 0.003 0.000 ARG D 694 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 160 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 MET cc_start: 0.4553 (pmm) cc_final: 0.3726 (pmm) REVERT: A 340 ASN cc_start: 0.7036 (OUTLIER) cc_final: 0.6746 (p0) REVERT: A 473 PHE cc_start: 0.6741 (m-80) cc_final: 0.6192 (m-80) REVERT: A 524 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8096 (p90) REVERT: A 609 TRP cc_start: 0.8326 (m100) cc_final: 0.8059 (m100) REVERT: A 789 GLU cc_start: 0.8039 (mp0) cc_final: 0.7754 (mp0) REVERT: A 817 MET cc_start: 0.5397 (mpp) cc_final: 0.4512 (mtm) REVERT: A 828 MET cc_start: 0.7473 (mpp) cc_final: 0.6887 (tpp) REVERT: B 28 ASN cc_start: 0.6160 (OUTLIER) cc_final: 0.4956 (t0) REVERT: B 74 MET cc_start: 0.7292 (ppp) cc_final: 0.6945 (ppp) REVERT: B 354 MET cc_start: 0.8296 (tpp) cc_final: 0.7834 (tpp) REVERT: B 378 LYS cc_start: 0.6898 (tptp) cc_final: 0.6522 (tptp) REVERT: B 392 TYR cc_start: 0.7654 (m-10) cc_final: 0.7450 (m-10) REVERT: B 611 TRP cc_start: 0.6018 (m100) cc_final: 0.5713 (m100) REVERT: B 692 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6453 (t80) REVERT: B 813 MET cc_start: 0.7960 (mpp) cc_final: 0.7551 (tmm) REVERT: C 473 PHE cc_start: 0.6742 (m-80) cc_final: 0.6201 (m-80) REVERT: C 524 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.8104 (p90) REVERT: C 637 PHE cc_start: 0.8718 (t80) cc_final: 0.8058 (m-80) REVERT: C 789 GLU cc_start: 0.8115 (mp0) cc_final: 0.7858 (mp0) REVERT: C 817 MET cc_start: 0.5177 (mpp) cc_final: 0.4764 (mtm) REVERT: C 828 MET cc_start: 0.8674 (tpp) cc_final: 0.8385 (mtt) REVERT: D 354 MET cc_start: 0.8318 (tpp) cc_final: 0.7824 (tpp) REVERT: D 378 LYS cc_start: 0.6817 (tptp) cc_final: 0.6379 (tptp) REVERT: D 611 TRP cc_start: 0.6060 (m100) cc_final: 0.5740 (m100) REVERT: D 697 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8457 (p) outliers start: 52 outliers final: 44 residues processed: 207 average time/residue: 0.3172 time to fit residues: 109.3807 Evaluate side-chains 205 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 155 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 198 TRP Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 794 CYS Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 692 TYR Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 697 VAL Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.9980 chunk 292 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 138 optimal weight: 0.0470 chunk 203 optimal weight: 4.9990 chunk 306 optimal weight: 7.9990 chunk 282 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 188 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN ** D 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25154 Z= 0.151 Angle : 0.609 14.548 34112 Z= 0.297 Chirality : 0.044 0.294 3906 Planarity : 0.003 0.038 4296 Dihedral : 4.605 49.514 3703 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.71 % Rotamer: Outliers : 2.05 % Allowed : 17.12 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 3066 helix: 1.13 (0.15), residues: 1284 sheet: -0.66 (0.25), residues: 464 loop : -1.57 (0.18), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 151 HIS 0.005 0.001 HIS C 119 PHE 0.054 0.001 PHE A 183 TYR 0.023 0.001 TYR B 692 ARG 0.005 0.000 ARG D 755 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 160 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 MET cc_start: 0.4555 (pmm) cc_final: 0.3732 (pmm) REVERT: A 340 ASN cc_start: 0.6940 (OUTLIER) cc_final: 0.6652 (p0) REVERT: A 524 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.8013 (p90) REVERT: A 536 MET cc_start: 0.8499 (tpp) cc_final: 0.8273 (tpt) REVERT: A 609 TRP cc_start: 0.8329 (m100) cc_final: 0.8054 (m100) REVERT: A 817 MET cc_start: 0.5467 (mpp) cc_final: 0.4603 (mtm) REVERT: A 828 MET cc_start: 0.7295 (mpp) cc_final: 0.6545 (tpp) REVERT: B 74 MET cc_start: 0.7186 (ppp) cc_final: 0.6849 (ppp) REVERT: B 354 MET cc_start: 0.8284 (tpp) cc_final: 0.7847 (tpp) REVERT: B 378 LYS cc_start: 0.6781 (tptp) cc_final: 0.6447 (tptp) REVERT: B 611 TRP cc_start: 0.5973 (m100) cc_final: 0.5681 (m100) REVERT: B 692 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6602 (t80) REVERT: B 813 MET cc_start: 0.7949 (mpp) cc_final: 0.7563 (tmm) REVERT: C 340 ASN cc_start: 0.7080 (OUTLIER) cc_final: 0.6847 (p0) REVERT: C 473 PHE cc_start: 0.6748 (m-80) cc_final: 0.6300 (m-80) REVERT: C 524 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.8002 (p90) REVERT: C 536 MET cc_start: 0.8457 (tpp) cc_final: 0.8254 (tpt) REVERT: C 637 PHE cc_start: 0.8714 (t80) cc_final: 0.8041 (m-10) REVERT: C 789 GLU cc_start: 0.8095 (mp0) cc_final: 0.7769 (mp0) REVERT: C 817 MET cc_start: 0.5178 (mpp) cc_final: 0.4765 (mtm) REVERT: C 828 MET cc_start: 0.8652 (tpp) cc_final: 0.8381 (mtt) REVERT: D 74 MET cc_start: 0.7454 (ppp) cc_final: 0.7234 (ppp) REVERT: D 354 MET cc_start: 0.8304 (tpp) cc_final: 0.7814 (tpp) REVERT: D 378 LYS cc_start: 0.6802 (tptp) cc_final: 0.6321 (tptp) REVERT: D 611 TRP cc_start: 0.6094 (m100) cc_final: 0.5768 (m100) REVERT: D 697 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8378 (p) outliers start: 54 outliers final: 43 residues processed: 207 average time/residue: 0.3294 time to fit residues: 111.5228 Evaluate side-chains 202 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 153 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 198 TRP Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 794 CYS Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 692 TYR Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 697 VAL Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 5.9990 chunk 260 optimal weight: 0.8980 chunk 74 optimal weight: 0.3980 chunk 225 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 67 optimal weight: 0.0770 chunk 244 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 251 optimal weight: 0.1980 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.072030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.053590 restraints weight = 145663.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.054930 restraints weight = 84187.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.055855 restraints weight = 59632.828| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25154 Z= 0.145 Angle : 0.608 14.969 34112 Z= 0.296 Chirality : 0.043 0.298 3906 Planarity : 0.003 0.037 4296 Dihedral : 4.361 46.761 3703 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.54 % Favored : 94.39 % Rotamer: Outliers : 1.93 % Allowed : 17.31 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 3066 helix: 1.15 (0.15), residues: 1280 sheet: -0.63 (0.25), residues: 470 loop : -1.55 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 151 HIS 0.006 0.001 HIS D 705 PHE 0.053 0.001 PHE A 183 TYR 0.021 0.001 TYR B 692 ARG 0.003 0.000 ARG D 694 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4140.78 seconds wall clock time: 76 minutes 50.59 seconds (4610.59 seconds total)