Starting phenix.real_space_refine on Sun Mar 17 18:17:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk1_33240/03_2024/7xk1_33240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk1_33240/03_2024/7xk1_33240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk1_33240/03_2024/7xk1_33240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk1_33240/03_2024/7xk1_33240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk1_33240/03_2024/7xk1_33240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk1_33240/03_2024/7xk1_33240_updated.pdb" } resolution = 4.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 150 5.49 5 S 62 5.16 5 C 11236 2.51 5 N 3188 2.21 5 O 3916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 880": "OD1" <-> "OD2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 880": "OD1" <-> "OD2" Residue "C GLU 961": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18552 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7711 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 58 Conformer: "B" Number of residues, atoms: 983, 7711 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 58 bond proxies already assigned to first conformer: 7862 Chain: "B" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1560 Unusual residues: {'GTP': 1} Classifications: {'RNA': 72, 'undetermined': 1} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 33} Link IDs: {'rna2p': 8, 'rna3p': 63, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" C B 2 " Chain: "C" Number of atoms: 7716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7711 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 58 Conformer: "B" Number of residues, atoms: 983, 7711 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 58 bond proxies already assigned to first conformer: 7862 Chain: "D" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1560 Unusual residues: {'GTP': 1} Classifications: {'RNA': 72, 'undetermined': 1} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 33} Link IDs: {'rna2p': 8, 'rna3p': 63, None: 1} Not linked: pdbres="GTP D 1 " pdbres=" C D 2 " Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AALA A 940 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 940 " occ=0.50 residue: pdb=" N AALA C 940 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA C 940 " occ=0.50 Time building chain proxies: 16.63, per 1000 atoms: 0.90 Number of scatterers: 18552 At special positions: 0 Unit cell: (204.6, 169.4, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 150 15.00 O 3916 8.00 N 3188 7.00 C 11236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS C 95 " distance=2.54 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.19 Conformation dependent library (CDL) restraints added in 5.4 seconds 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 8 sheets defined 46.8% alpha, 8.4% beta 32 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 8.18 Creating SS restraints... Processing helix chain 'A' and resid 74 through 88 removed outlier: 3.814A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TRP A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.996A pdb=" N PHE A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 removed outlier: 4.123A pdb=" N LEU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 removed outlier: 3.844A pdb=" N GLU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N MET A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 297 removed outlier: 3.692A pdb=" N GLN A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 320 removed outlier: 3.555A pdb=" N VAL A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 353 removed outlier: 4.346A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 417 removed outlier: 3.538A pdb=" N LYS A 405 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN A 413 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 460 No H-bonds generated for 'chain 'A' and resid 457 through 460' Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 509 through 520 Proline residue: A 516 - end of helix removed outlier: 3.642A pdb=" N SER A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 3.573A pdb=" N GLU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 612 removed outlier: 4.282A pdb=" N LYS A 601 " --> pdb=" O MET A 597 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 610 " --> pdb=" O HIS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 632 removed outlier: 4.119A pdb=" N GLU A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 631 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 648 Processing helix chain 'A' and resid 652 through 661 removed outlier: 3.677A pdb=" N ILE A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 715 removed outlier: 3.587A pdb=" N ARG A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 700 " --> pdb=" O GLY A 696 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 724 removed outlier: 3.912A pdb=" N ARG A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 720 through 724' Processing helix chain 'A' and resid 726 through 729 removed outlier: 4.301A pdb=" N SER A 729 " --> pdb=" O GLN A 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 726 through 729' Processing helix chain 'A' and resid 739 through 756 removed outlier: 5.065A pdb=" N ALA A 751 " --> pdb=" O GLU A 747 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 753 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 772 Proline residue: A 765 - end of helix removed outlier: 4.441A pdb=" N ALA A 771 " --> pdb=" O LYS A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 782 through 785 No H-bonds generated for 'chain 'A' and resid 782 through 785' Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 793 through 801 Processing helix chain 'A' and resid 805 through 814 removed outlier: 3.956A pdb=" N GLU A 809 " --> pdb=" O GLU A 805 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA A 810 " --> pdb=" O GLN A 806 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 847 removed outlier: 3.619A pdb=" N VAL A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 873 Processing helix chain 'A' and resid 881 through 891 removed outlier: 4.097A pdb=" N THR A 886 " --> pdb=" O THR A 882 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 887 " --> pdb=" O LYS A 883 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 918 removed outlier: 3.848A pdb=" N ASP A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP A 918 " --> pdb=" O GLN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 929 removed outlier: 3.581A pdb=" N SER A 928 " --> pdb=" O GLU A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 952 removed outlier: 4.003A pdb=" N GLU A 946 " --> pdb=" O GLN A 942 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 948 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG A 952 " --> pdb=" O GLU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 970 removed outlier: 3.753A pdb=" N SER A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Proline residue: A 966 - end of helix removed outlier: 4.260A pdb=" N ILE A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 970 " --> pdb=" O PRO A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 977 No H-bonds generated for 'chain 'A' and resid 975 through 977' Processing helix chain 'A' and resid 989 through 1003 removed outlier: 3.856A pdb=" N ASP A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1031 removed outlier: 4.961A pdb=" N GLU A1020 " --> pdb=" O ASP A1016 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) Proline residue: A1024 - end of helix removed outlier: 3.927A pdb=" N ASP A1027 " --> pdb=" O GLN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1053 Processing helix chain 'C' and resid 74 through 88 removed outlier: 3.815A pdb=" N ILE C 78 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN C 79 " --> pdb=" O GLN C 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 84 " --> pdb=" O ARG C 80 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.996A pdb=" N PHE C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU C 164 " --> pdb=" O GLN C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 239 removed outlier: 4.122A pdb=" N LEU C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 273 removed outlier: 3.748A pdb=" N GLU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N MET C 267 " --> pdb=" O ASN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 297 removed outlier: 3.694A pdb=" N GLN C 281 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS C 282 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP C 285 " --> pdb=" O GLN C 281 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 320 removed outlier: 3.556A pdb=" N VAL C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 308 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 353 removed outlier: 4.346A pdb=" N LEU C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS C 348 " --> pdb=" O GLN C 344 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 417 removed outlier: 3.537A pdb=" N LYS C 405 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 410 " --> pdb=" O GLN C 406 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 413 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE C 414 " --> pdb=" O SER C 410 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 415 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 460 No H-bonds generated for 'chain 'C' and resid 457 through 460' Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'C' and resid 509 through 520 Proline residue: C 516 - end of helix removed outlier: 3.643A pdb=" N SER C 520 " --> pdb=" O PRO C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 590 removed outlier: 3.573A pdb=" N GLU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 612 removed outlier: 4.281A pdb=" N LYS C 601 " --> pdb=" O MET C 597 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 602 " --> pdb=" O GLN C 598 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS C 606 " --> pdb=" O GLN C 602 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP C 607 " --> pdb=" O ARG C 603 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE C 610 " --> pdb=" O HIS C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 632 removed outlier: 4.118A pdb=" N GLU C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN C 631 " --> pdb=" O GLN C 627 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 632 " --> pdb=" O GLU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 648 Processing helix chain 'C' and resid 652 through 661 removed outlier: 3.677A pdb=" N ILE C 656 " --> pdb=" O LYS C 652 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR C 657 " --> pdb=" O ASP C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 715 removed outlier: 3.587A pdb=" N ARG C 694 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA C 699 " --> pdb=" O LYS C 695 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL C 700 " --> pdb=" O GLY C 696 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 703 " --> pdb=" O ALA C 699 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C 707 " --> pdb=" O ALA C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 724 removed outlier: 3.912A pdb=" N ARG C 724 " --> pdb=" O LEU C 720 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 720 through 724' Processing helix chain 'C' and resid 726 through 729 removed outlier: 4.300A pdb=" N SER C 729 " --> pdb=" O GLN C 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 726 through 729' Processing helix chain 'C' and resid 739 through 756 removed outlier: 5.065A pdb=" N ALA C 751 " --> pdb=" O GLU C 747 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 753 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 772 Proline residue: C 765 - end of helix removed outlier: 4.441A pdb=" N ALA C 771 " --> pdb=" O LYS C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 779 No H-bonds generated for 'chain 'C' and resid 777 through 779' Processing helix chain 'C' and resid 782 through 785 No H-bonds generated for 'chain 'C' and resid 782 through 785' Processing helix chain 'C' and resid 787 through 789 No H-bonds generated for 'chain 'C' and resid 787 through 789' Processing helix chain 'C' and resid 793 through 801 Processing helix chain 'C' and resid 805 through 814 removed outlier: 3.956A pdb=" N GLU C 809 " --> pdb=" O GLU C 805 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA C 810 " --> pdb=" O GLN C 806 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 847 removed outlier: 3.620A pdb=" N VAL C 832 " --> pdb=" O ASP C 828 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 833 " --> pdb=" O PRO C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 873 Processing helix chain 'C' and resid 881 through 891 removed outlier: 4.097A pdb=" N THR C 886 " --> pdb=" O THR C 882 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 887 " --> pdb=" O LYS C 883 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU C 891 " --> pdb=" O LEU C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 918 removed outlier: 3.848A pdb=" N ASP C 902 " --> pdb=" O SER C 898 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP C 918 " --> pdb=" O GLN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 929 removed outlier: 3.580A pdb=" N SER C 928 " --> pdb=" O GLU C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 952 removed outlier: 4.004A pdb=" N GLU C 946 " --> pdb=" O GLN C 942 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 948 " --> pdb=" O ALA C 944 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA C 949 " --> pdb=" O ILE C 945 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG C 952 " --> pdb=" O GLU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 970 removed outlier: 3.754A pdb=" N SER C 964 " --> pdb=" O VAL C 960 " (cutoff:3.500A) Proline residue: C 966 - end of helix removed outlier: 4.206A pdb=" N ILE C 969 " --> pdb=" O ARG C 965 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 970 " --> pdb=" O PRO C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 977 No H-bonds generated for 'chain 'C' and resid 975 through 977' Processing helix chain 'C' and resid 989 through 1003 removed outlier: 3.856A pdb=" N ASP C1003 " --> pdb=" O LEU C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1014 through 1031 removed outlier: 4.963A pdb=" N GLU C1020 " --> pdb=" O ASP C1016 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU C1021 " --> pdb=" O ALA C1017 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C1022 " --> pdb=" O SER C1018 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN C1023 " --> pdb=" O LEU C1019 " (cutoff:3.500A) Proline residue: C1024 - end of helix removed outlier: 3.926A pdb=" N ASP C1027 " --> pdb=" O GLN C1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1053 Processing sheet with id= A, first strand: chain 'A' and resid 119 through 128 removed outlier: 4.057A pdb=" N THR A 208 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP A 194 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 425 through 430 removed outlier: 3.776A pdb=" N LEU A 434 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 390 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 617 through 619 Processing sheet with id= D, first strand: chain 'A' and resid 636 through 642 removed outlier: 4.023A pdb=" N MET A 637 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 119 through 128 removed outlier: 4.056A pdb=" N THR C 208 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP C 194 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 425 through 430 removed outlier: 3.776A pdb=" N LEU C 434 " --> pdb=" O ILE C 390 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 390 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 617 through 619 Processing sheet with id= H, first strand: chain 'C' and resid 636 through 642 removed outlier: 4.023A pdb=" N MET C 637 " --> pdb=" O ALA C 684 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1556 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 87 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 7.61 Time building geometry restraints manager: 8.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2820 1.31 - 1.44: 5792 1.44 - 1.56: 10216 1.56 - 1.69: 296 1.69 - 1.81: 104 Bond restraints: 19228 Sorted by residual: bond pdb=" C2 GTP D 1 " pdb=" N2 GTP D 1 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.453 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" N ILE A 969 " pdb=" CA ILE A 969 " ideal model delta sigma weight residual 1.459 1.505 -0.047 1.28e-02 6.10e+03 1.32e+01 bond pdb=" N THR A 967 " pdb=" CA THR A 967 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" N THR C 967 " pdb=" CA THR C 967 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.03e+01 ... (remaining 19223 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.87: 1301 106.87 - 113.66: 10843 113.66 - 120.45: 7592 120.45 - 127.23: 6629 127.23 - 134.02: 417 Bond angle restraints: 26782 Sorted by residual: angle pdb=" N ARG C 965 " pdb=" CA ARG C 965 " pdb=" C ARG C 965 " ideal model delta sigma weight residual 112.75 103.94 8.81 1.36e+00 5.41e-01 4.19e+01 angle pdb=" N ARG A 965 " pdb=" CA ARG A 965 " pdb=" C ARG A 965 " ideal model delta sigma weight residual 112.75 103.97 8.78 1.36e+00 5.41e-01 4.17e+01 angle pdb=" C PRO A 966 " pdb=" CA PRO A 966 " pdb=" CB PRO A 966 " ideal model delta sigma weight residual 112.64 105.71 6.93 1.74e+00 3.30e-01 1.59e+01 angle pdb=" C PRO C 966 " pdb=" CA PRO C 966 " pdb=" CB PRO C 966 " ideal model delta sigma weight residual 112.64 105.74 6.90 1.74e+00 3.30e-01 1.57e+01 angle pdb=" N ASN C 97 " pdb=" CA ASN C 97 " pdb=" C ASN C 97 " ideal model delta sigma weight residual 112.13 106.88 5.25 1.37e+00 5.33e-01 1.47e+01 ... (remaining 26777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.00: 11161 30.00 - 59.99: 494 59.99 - 89.99: 132 89.99 - 119.98: 4 119.98 - 149.98: 2 Dihedral angle restraints: 11793 sinusoidal: 6077 harmonic: 5716 Sorted by residual: dihedral pdb=" O4' U D 19 " pdb=" C1' U D 19 " pdb=" N1 U D 19 " pdb=" C2 U D 19 " ideal model delta sinusoidal sigma weight residual 200.00 50.02 149.98 1 1.50e+01 4.44e-03 7.96e+01 dihedral pdb=" O4' U B 19 " pdb=" C1' U B 19 " pdb=" N1 U B 19 " pdb=" C2 U B 19 " ideal model delta sinusoidal sigma weight residual 200.00 50.07 149.93 1 1.50e+01 4.44e-03 7.96e+01 dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 6.22 98.37 1 2.00e+01 2.50e-03 2.75e+01 ... (remaining 11790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2847 0.068 - 0.136: 283 0.136 - 0.205: 18 0.205 - 0.273: 4 0.273 - 0.341: 2 Chirality restraints: 3154 Sorted by residual: chirality pdb=" P G D 33 " pdb=" OP1 G D 33 " pdb=" OP2 G D 33 " pdb=" O5' G D 33 " both_signs ideal model delta sigma weight residual True 2.41 -2.75 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" P G D 38 " pdb=" OP1 G D 38 " pdb=" OP2 G D 38 " pdb=" O5' G D 38 " both_signs ideal model delta sigma weight residual True 2.41 -2.73 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB ILE A 969 " pdb=" CA ILE A 969 " pdb=" CG1 ILE A 969 " pdb=" CG2 ILE A 969 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 3151 not shown) Planarity restraints: 2922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 637 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO C 638 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 638 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 638 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 637 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 638 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C1063 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C SER C1063 " 0.027 2.00e-02 2.50e+03 pdb=" O SER C1063 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL C1064 " -0.009 2.00e-02 2.50e+03 ... (remaining 2919 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2650 2.75 - 3.29: 17882 3.29 - 3.83: 30865 3.83 - 4.36: 34965 4.36 - 4.90: 56935 Nonbonded interactions: 143297 Sorted by model distance: nonbonded pdb=" O PHE C 950 " pdb=" OG1 THR C 953 " model vdw 2.217 2.440 nonbonded pdb=" O PHE A 950 " pdb=" OG1 THR A 953 " model vdw 2.218 2.440 nonbonded pdb=" O GLU C 206 " pdb=" NH1 ARG C 234 " model vdw 2.241 2.520 nonbonded pdb=" O GLU A 206 " pdb=" NH1 ARG A 234 " model vdw 2.241 2.520 nonbonded pdb=" OE1 GLU C 389 " pdb=" OH TYR C 584 " model vdw 2.245 2.440 ... (remaining 143292 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' and (resid 70 through 939 or resid 941 through 1068)) selection = (chain 'C' and (resid 70 through 939 or resid 941 through 1068)) } 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=0.50 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: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.340 Check model and map are aligned: 0.210 Set scattering table: 0.150 Process input model: 64.890 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.130 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 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 : 0.004 0.124 19228 Z= 0.253 Angle : 0.611 9.146 26782 Z= 0.337 Chirality : 0.042 0.341 3154 Planarity : 0.004 0.043 2922 Dihedral : 16.551 149.977 8094 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.07 % Allowed : 8.37 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 1964 helix: -0.14 (0.18), residues: 878 sheet: -0.34 (0.37), residues: 238 loop : -1.60 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 194 HIS 0.004 0.001 HIS C 145 PHE 0.010 0.001 PHE A 544 TYR 0.013 0.001 TYR A 230 ARG 0.002 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 394 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.5538 (m) cc_final: 0.4597 (t) REVERT: A 153 LYS cc_start: 0.4172 (ttpt) cc_final: 0.3502 (tttt) REVERT: A 167 LEU cc_start: 0.8187 (tp) cc_final: 0.7888 (tp) REVERT: A 332 PHE cc_start: 0.6005 (m-80) cc_final: 0.5753 (m-80) REVERT: A 495 TYR cc_start: 0.6155 (OUTLIER) cc_final: 0.5900 (m-80) REVERT: A 619 ILE cc_start: 0.9080 (pt) cc_final: 0.8777 (mp) REVERT: A 869 VAL cc_start: 0.9310 (m) cc_final: 0.9054 (p) REVERT: C 254 ILE cc_start: 0.8910 (pt) cc_final: 0.8589 (tp) REVERT: C 280 ILE cc_start: 0.7104 (mm) cc_final: 0.6891 (mm) REVERT: C 305 ASP cc_start: 0.6896 (t70) cc_final: 0.6683 (t70) REVERT: C 341 GLN cc_start: 0.7792 (pt0) cc_final: 0.7145 (tt0) REVERT: C 495 TYR cc_start: 0.5641 (OUTLIER) cc_final: 0.4673 (m-80) REVERT: C 655 LEU cc_start: 0.8661 (mt) cc_final: 0.8064 (tt) REVERT: C 741 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7372 (p0) REVERT: C 743 MET cc_start: 0.8721 (mmt) cc_final: 0.8472 (mmp) REVERT: C 775 MET cc_start: 0.8697 (tmm) cc_final: 0.8092 (tmm) REVERT: C 866 TYR cc_start: 0.8390 (t80) cc_final: 0.8164 (t80) outliers start: 51 outliers final: 2 residues processed: 436 average time/residue: 0.3243 time to fit residues: 206.3997 Evaluate side-chains 191 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 186 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 122 optimal weight: 0.0980 chunk 190 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 GLN C 76 GLN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN C 312 HIS C 341 GLN C 352 ASN ** C 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19228 Z= 0.202 Angle : 0.635 11.744 26782 Z= 0.318 Chirality : 0.043 0.244 3154 Planarity : 0.004 0.041 2922 Dihedral : 17.644 150.710 4396 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.40 % Rotamer: Outliers : 0.06 % Allowed : 1.75 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.19), residues: 1964 helix: -0.22 (0.18), residues: 880 sheet: -0.30 (0.35), residues: 226 loop : -1.54 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 198 HIS 0.010 0.001 HIS C 165 PHE 0.034 0.002 PHE C 710 TYR 0.021 0.002 TYR C 360 ARG 0.006 0.001 ARG A 927 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 1.784 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 167 LEU cc_start: 0.8398 (tp) cc_final: 0.8014 (tp) REVERT: A 183 GLU cc_start: 0.8227 (tm-30) cc_final: 0.8016 (tm-30) REVERT: A 314 PHE cc_start: 0.8085 (t80) cc_final: 0.7870 (t80) REVERT: A 332 PHE cc_start: 0.6251 (m-80) cc_final: 0.5850 (m-80) REVERT: A 389 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7841 (tm-30) REVERT: A 573 LEU cc_start: 0.8373 (tp) cc_final: 0.8058 (tt) REVERT: A 619 ILE cc_start: 0.9072 (pt) cc_final: 0.8759 (mp) REVERT: A 842 LEU cc_start: 0.8811 (pp) cc_final: 0.8572 (pp) REVERT: A 869 VAL cc_start: 0.9270 (m) cc_final: 0.8859 (p) REVERT: C 199 GLU cc_start: 0.7489 (pt0) cc_final: 0.7264 (mt-10) REVERT: C 205 MET cc_start: 0.7139 (mmm) cc_final: 0.6812 (mmm) REVERT: C 280 ILE cc_start: 0.7175 (mm) cc_final: 0.6931 (mm) REVERT: C 305 ASP cc_start: 0.6770 (t70) cc_final: 0.6415 (t70) REVERT: C 341 GLN cc_start: 0.7812 (pt0) cc_final: 0.7539 (tt0) REVERT: C 655 LEU cc_start: 0.8694 (mt) cc_final: 0.8254 (tt) REVERT: C 730 ILE cc_start: 0.8349 (tt) cc_final: 0.8124 (tt) REVERT: C 866 TYR cc_start: 0.8420 (t80) cc_final: 0.8210 (t80) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.2939 time to fit residues: 105.2373 Evaluate side-chains 156 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 191 optimal weight: 0.0980 chunk 206 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 153 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN C 76 GLN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN ** C 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 GLN C 697 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19228 Z= 0.233 Angle : 0.615 8.471 26782 Z= 0.312 Chirality : 0.041 0.200 3154 Planarity : 0.004 0.044 2922 Dihedral : 17.532 152.325 4396 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.24 % Allowed : 2.17 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 1964 helix: -0.40 (0.18), residues: 884 sheet: -0.48 (0.34), residues: 232 loop : -1.40 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 198 HIS 0.007 0.001 HIS A 274 PHE 0.034 0.002 PHE C 710 TYR 0.026 0.002 TYR A 230 ARG 0.008 0.001 ARG A 735 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.7954 (mpp) cc_final: 0.7579 (mpt) REVERT: A 178 ASP cc_start: 0.7663 (t0) cc_final: 0.7336 (t0) REVERT: A 233 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7817 (tm-30) REVERT: A 332 PHE cc_start: 0.6640 (m-80) cc_final: 0.6117 (m-80) REVERT: A 619 ILE cc_start: 0.9103 (pt) cc_final: 0.8852 (mp) REVERT: A 842 LEU cc_start: 0.8825 (pp) cc_final: 0.8563 (pp) REVERT: A 869 VAL cc_start: 0.9308 (m) cc_final: 0.8873 (p) REVERT: C 199 GLU cc_start: 0.7714 (pt0) cc_final: 0.7359 (mt-10) REVERT: C 305 ASP cc_start: 0.6985 (t70) cc_final: 0.6696 (t70) REVERT: C 655 LEU cc_start: 0.9000 (mt) cc_final: 0.8304 (tt) REVERT: C 705 TYR cc_start: 0.9039 (m-10) cc_final: 0.8232 (m-10) REVERT: C 866 TYR cc_start: 0.8594 (t80) cc_final: 0.8065 (t80) REVERT: C 914 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8759 (tm-30) outliers start: 4 outliers final: 1 residues processed: 192 average time/residue: 0.2783 time to fit residues: 83.7209 Evaluate side-chains 121 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 202 optimal weight: 0.0570 chunk 100 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 54 optimal weight: 0.0870 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS A 341 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN A 733 HIS C 76 GLN C 97 ASN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19228 Z= 0.190 Angle : 0.593 8.898 26782 Z= 0.293 Chirality : 0.040 0.182 3154 Planarity : 0.004 0.039 2922 Dihedral : 17.484 153.497 4396 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.12 % Allowed : 1.45 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.19), residues: 1964 helix: -0.21 (0.18), residues: 884 sheet: -0.70 (0.35), residues: 226 loop : -1.36 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 530 HIS 0.005 0.001 HIS C 165 PHE 0.022 0.001 PHE A 210 TYR 0.021 0.002 TYR A 230 ARG 0.006 0.000 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 1.900 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 93 MET cc_start: 0.7980 (mpp) cc_final: 0.7636 (mpp) REVERT: A 332 PHE cc_start: 0.6742 (m-80) cc_final: 0.6128 (m-80) REVERT: A 528 MET cc_start: 0.8204 (ppp) cc_final: 0.7742 (ppp) REVERT: A 619 ILE cc_start: 0.9107 (pt) cc_final: 0.8831 (mp) REVERT: A 869 VAL cc_start: 0.9305 (m) cc_final: 0.8951 (p) REVERT: C 199 GLU cc_start: 0.7694 (pt0) cc_final: 0.7389 (mt-10) REVERT: C 655 LEU cc_start: 0.9073 (mt) cc_final: 0.8452 (tt) REVERT: C 866 TYR cc_start: 0.8636 (t80) cc_final: 0.8026 (t80) REVERT: C 914 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8809 (tm-30) outliers start: 2 outliers final: 0 residues processed: 177 average time/residue: 0.2856 time to fit residues: 80.4798 Evaluate side-chains 120 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN A 733 HIS A 942 GLN C 97 ASN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 HIS C 478 ASN C 570 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19228 Z= 0.310 Angle : 0.672 10.828 26782 Z= 0.339 Chirality : 0.043 0.187 3154 Planarity : 0.005 0.049 2922 Dihedral : 17.663 153.491 4396 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.06 % Allowed : 2.35 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 1964 helix: -0.39 (0.17), residues: 906 sheet: -1.01 (0.35), residues: 232 loop : -1.39 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 194 HIS 0.040 0.002 HIS C 312 PHE 0.039 0.002 PHE A 210 TYR 0.032 0.003 TYR A 230 ARG 0.006 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 1.760 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 93 MET cc_start: 0.8271 (mpp) cc_final: 0.8023 (mpp) REVERT: A 280 ILE cc_start: 0.8242 (mm) cc_final: 0.7915 (mm) REVERT: A 528 MET cc_start: 0.8344 (ppp) cc_final: 0.7805 (ppp) REVERT: A 619 ILE cc_start: 0.9124 (pt) cc_final: 0.8895 (mp) REVERT: A 743 MET cc_start: 0.8384 (mmp) cc_final: 0.8038 (mmp) REVERT: A 775 MET cc_start: 0.8484 (tmm) cc_final: 0.7666 (tmm) REVERT: C 199 GLU cc_start: 0.7835 (pt0) cc_final: 0.7299 (mt-10) REVERT: C 659 MET cc_start: 0.8817 (mtp) cc_final: 0.8177 (mtm) REVERT: C 866 TYR cc_start: 0.8796 (t80) cc_final: 0.8170 (t80) REVERT: C 887 LEU cc_start: 0.9151 (pp) cc_final: 0.8862 (pp) REVERT: C 914 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8883 (tm-30) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.2902 time to fit residues: 70.3107 Evaluate side-chains 115 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN A 733 HIS ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19228 Z= 0.274 Angle : 0.635 9.643 26782 Z= 0.319 Chirality : 0.041 0.182 3154 Planarity : 0.004 0.055 2922 Dihedral : 17.689 153.853 4396 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.06 % Allowed : 1.08 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 1964 helix: -0.33 (0.17), residues: 910 sheet: -1.04 (0.34), residues: 232 loop : -1.33 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 198 HIS 0.007 0.001 HIS C 312 PHE 0.028 0.002 PHE C 710 TYR 0.029 0.002 TYR A 230 ARG 0.005 0.001 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ILE cc_start: 0.8316 (mm) cc_final: 0.7976 (mm) REVERT: A 528 MET cc_start: 0.8283 (ppp) cc_final: 0.7746 (ppp) REVERT: A 619 ILE cc_start: 0.9132 (pt) cc_final: 0.8843 (mp) REVERT: A 743 MET cc_start: 0.8389 (mmp) cc_final: 0.8010 (mmp) REVERT: A 775 MET cc_start: 0.8427 (tmm) cc_final: 0.7452 (tmm) REVERT: C 143 GLN cc_start: 0.7333 (tt0) cc_final: 0.7010 (tt0) REVERT: C 199 GLU cc_start: 0.7813 (pt0) cc_final: 0.7394 (mt-10) REVERT: C 273 GLU cc_start: 0.7691 (pm20) cc_final: 0.7484 (pm20) REVERT: C 659 MET cc_start: 0.8819 (mtp) cc_final: 0.8465 (mtm) REVERT: C 866 TYR cc_start: 0.8781 (t80) cc_final: 0.8129 (t80) REVERT: C 887 LEU cc_start: 0.9168 (pp) cc_final: 0.8888 (pp) REVERT: C 914 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8849 (tm-30) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.2916 time to fit residues: 71.6686 Evaluate side-chains 120 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 115 optimal weight: 0.1980 chunk 148 optimal weight: 0.0060 chunk 114 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 202 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 HIS C 76 GLN C 149 GLN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19228 Z= 0.155 Angle : 0.583 10.266 26782 Z= 0.285 Chirality : 0.040 0.196 3154 Planarity : 0.004 0.041 2922 Dihedral : 17.566 154.605 4396 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 1964 helix: -0.09 (0.17), residues: 910 sheet: -0.56 (0.35), residues: 216 loop : -1.30 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 201 HIS 0.006 0.001 HIS C 145 PHE 0.034 0.001 PHE C 710 TYR 0.020 0.001 TYR A 230 ARG 0.009 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8013 (mpp) cc_final: 0.7658 (mpp) REVERT: A 280 ILE cc_start: 0.8205 (mm) cc_final: 0.7876 (mm) REVERT: A 528 MET cc_start: 0.8202 (ppp) cc_final: 0.7615 (ppp) REVERT: A 619 ILE cc_start: 0.9104 (pt) cc_final: 0.8814 (mp) REVERT: A 743 MET cc_start: 0.8390 (mmp) cc_final: 0.8001 (mmp) REVERT: A 775 MET cc_start: 0.8318 (tmm) cc_final: 0.7491 (tmm) REVERT: C 143 GLN cc_start: 0.7677 (tt0) cc_final: 0.7477 (tt0) REVERT: C 199 GLU cc_start: 0.7904 (pt0) cc_final: 0.7544 (mt-10) REVERT: C 290 GLU cc_start: 0.7748 (pt0) cc_final: 0.7527 (pt0) REVERT: C 634 GLU cc_start: 0.7116 (tp30) cc_final: 0.6814 (tp30) REVERT: C 655 LEU cc_start: 0.9167 (mt) cc_final: 0.8623 (tt) REVERT: C 767 ILE cc_start: 0.9385 (pt) cc_final: 0.9096 (mt) REVERT: C 866 TYR cc_start: 0.8711 (t80) cc_final: 0.8337 (t80) REVERT: C 887 LEU cc_start: 0.9170 (pp) cc_final: 0.8885 (pp) REVERT: C 914 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8860 (tm-30) REVERT: C 947 MET cc_start: 0.8304 (tmm) cc_final: 0.8075 (tmm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2786 time to fit residues: 70.4839 Evaluate side-chains 120 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 0.0670 chunk 159 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 HIS ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.6125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19228 Z= 0.231 Angle : 0.616 9.677 26782 Z= 0.306 Chirality : 0.041 0.180 3154 Planarity : 0.004 0.041 2922 Dihedral : 17.585 154.386 4396 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.06 % Allowed : 0.66 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.99 (0.19), residues: 1964 helix: -0.02 (0.17), residues: 912 sheet: -0.67 (0.34), residues: 218 loop : -1.28 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 201 HIS 0.006 0.001 HIS C 283 PHE 0.034 0.002 PHE C 710 TYR 0.029 0.002 TYR A 230 ARG 0.003 0.000 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ILE cc_start: 0.8298 (mm) cc_final: 0.7988 (mm) REVERT: A 528 MET cc_start: 0.8234 (ppp) cc_final: 0.7638 (ppp) REVERT: A 619 ILE cc_start: 0.9100 (pt) cc_final: 0.8817 (mp) REVERT: A 775 MET cc_start: 0.8413 (tmm) cc_final: 0.7872 (tmm) REVERT: A 842 LEU cc_start: 0.8865 (pp) cc_final: 0.8636 (pp) REVERT: A 871 ILE cc_start: 0.9343 (tp) cc_final: 0.9111 (tp) REVERT: A 1035 MET cc_start: 0.4743 (mpp) cc_final: 0.4452 (mpp) REVERT: C 199 GLU cc_start: 0.7920 (pt0) cc_final: 0.7102 (mt-10) REVERT: C 206 GLU cc_start: 0.5693 (tt0) cc_final: 0.5492 (tt0) REVERT: C 659 MET cc_start: 0.8798 (mtp) cc_final: 0.8461 (mtm) REVERT: C 866 TYR cc_start: 0.8765 (t80) cc_final: 0.8134 (t80) REVERT: C 887 LEU cc_start: 0.9188 (pp) cc_final: 0.8924 (pp) REVERT: C 914 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8779 (tm-30) REVERT: C 947 MET cc_start: 0.8307 (tmm) cc_final: 0.7994 (tmm) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.3127 time to fit residues: 72.6146 Evaluate side-chains 114 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 148 optimal weight: 0.0070 chunk 57 optimal weight: 0.0970 chunk 170 optimal weight: 0.0770 chunk 178 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 123 optimal weight: 0.1980 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 341 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 HIS C 76 GLN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 HIS C 570 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19228 Z= 0.139 Angle : 0.588 9.644 26782 Z= 0.287 Chirality : 0.039 0.175 3154 Planarity : 0.004 0.034 2922 Dihedral : 17.464 155.165 4396 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.84 (0.19), residues: 1964 helix: 0.11 (0.18), residues: 910 sheet: -0.48 (0.35), residues: 212 loop : -1.25 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 542 HIS 0.007 0.001 HIS C 145 PHE 0.031 0.001 PHE C 710 TYR 0.014 0.001 TYR A 497 ARG 0.005 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.7944 (mpp) cc_final: 0.7740 (mpt) REVERT: A 280 ILE cc_start: 0.8185 (mm) cc_final: 0.7852 (mm) REVERT: A 528 MET cc_start: 0.8241 (ppp) cc_final: 0.7622 (ppp) REVERT: A 551 ILE cc_start: 0.8247 (tt) cc_final: 0.7987 (tt) REVERT: A 619 ILE cc_start: 0.9047 (pt) cc_final: 0.8741 (mp) REVERT: A 743 MET cc_start: 0.8469 (mmp) cc_final: 0.8074 (mmp) REVERT: A 775 MET cc_start: 0.8254 (tmm) cc_final: 0.7437 (tmm) REVERT: A 842 LEU cc_start: 0.8898 (pp) cc_final: 0.8656 (pp) REVERT: A 1035 MET cc_start: 0.4704 (mpp) cc_final: 0.4343 (mpp) REVERT: C 183 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7348 (tm-30) REVERT: C 199 GLU cc_start: 0.7898 (pt0) cc_final: 0.7117 (mt-10) REVERT: C 206 GLU cc_start: 0.5791 (tt0) cc_final: 0.5491 (tt0) REVERT: C 634 GLU cc_start: 0.7072 (tp30) cc_final: 0.6764 (tp30) REVERT: C 655 LEU cc_start: 0.9136 (mt) cc_final: 0.8616 (tt) REVERT: C 866 TYR cc_start: 0.8730 (t80) cc_final: 0.8324 (t80) REVERT: C 887 LEU cc_start: 0.9178 (pp) cc_final: 0.8899 (pp) REVERT: C 914 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8790 (tm-30) REVERT: C 947 MET cc_start: 0.8213 (tmm) cc_final: 0.7874 (tmm) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2856 time to fit residues: 72.5472 Evaluate side-chains 117 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 chunk 192 optimal weight: 0.6980 chunk 166 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 HIS C 76 GLN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19228 Z= 0.177 Angle : 0.595 9.620 26782 Z= 0.292 Chirality : 0.040 0.173 3154 Planarity : 0.004 0.034 2922 Dihedral : 17.450 154.865 4396 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.79 (0.19), residues: 1964 helix: 0.19 (0.18), residues: 910 sheet: -0.63 (0.34), residues: 218 loop : -1.22 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 HIS 0.005 0.001 HIS A 145 PHE 0.031 0.001 PHE C 710 TYR 0.023 0.002 TYR A 230 ARG 0.003 0.000 ARG C 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.7987 (mpp) cc_final: 0.7774 (mpt) REVERT: A 280 ILE cc_start: 0.8255 (mm) cc_final: 0.7938 (mm) REVERT: A 528 MET cc_start: 0.8220 (ppp) cc_final: 0.7644 (ppp) REVERT: A 551 ILE cc_start: 0.8271 (tt) cc_final: 0.8015 (tt) REVERT: A 619 ILE cc_start: 0.9061 (pt) cc_final: 0.8752 (mp) REVERT: A 775 MET cc_start: 0.8314 (tmm) cc_final: 0.7832 (tmm) REVERT: A 842 LEU cc_start: 0.8886 (pp) cc_final: 0.8632 (pp) REVERT: C 183 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7403 (tm-30) REVERT: C 199 GLU cc_start: 0.7850 (pt0) cc_final: 0.7205 (mt-10) REVERT: C 206 GLU cc_start: 0.5764 (tt0) cc_final: 0.5392 (tt0) REVERT: C 634 GLU cc_start: 0.7079 (tp30) cc_final: 0.6806 (tp30) REVERT: C 659 MET cc_start: 0.8748 (mtp) cc_final: 0.8410 (mtm) REVERT: C 866 TYR cc_start: 0.8753 (t80) cc_final: 0.8330 (t80) REVERT: C 887 LEU cc_start: 0.9194 (pp) cc_final: 0.8921 (pp) REVERT: C 914 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8812 (tm-30) REVERT: C 947 MET cc_start: 0.8296 (tmm) cc_final: 0.7917 (tmm) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2851 time to fit residues: 69.4327 Evaluate side-chains 112 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 2.9990 chunk 51 optimal weight: 0.0670 chunk 153 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 166 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 HIS C 76 GLN ** C 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.111739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.089223 restraints weight = 57922.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.086856 restraints weight = 85129.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.085099 restraints weight = 52758.281| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19228 Z= 0.152 Angle : 0.582 9.299 26782 Z= 0.284 Chirality : 0.039 0.170 3154 Planarity : 0.004 0.034 2922 Dihedral : 17.415 155.040 4396 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.06 % Allowed : 0.30 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.72 (0.19), residues: 1964 helix: 0.23 (0.18), residues: 908 sheet: -0.43 (0.35), residues: 212 loop : -1.20 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 542 HIS 0.005 0.001 HIS A 145 PHE 0.030 0.001 PHE C 710 TYR 0.017 0.001 TYR A 230 ARG 0.003 0.000 ARG A 642 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3289.56 seconds wall clock time: 60 minutes 30.54 seconds (3630.54 seconds total)