Starting phenix.real_space_refine on Sun Mar 17 17:28:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1c_34427/03_2024/8h1c_34427_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1c_34427/03_2024/8h1c_34427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1c_34427/03_2024/8h1c_34427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1c_34427/03_2024/8h1c_34427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1c_34427/03_2024/8h1c_34427_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1c_34427/03_2024/8h1c_34427_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.054 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 148 5.49 5 S 62 5.16 5 C 11199 2.51 5 N 3182 2.21 5 O 3892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 961": "OE1" <-> "OE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A ARG 965": "NH1" <-> "NH2" Residue "A GLU 991": "OE1" <-> "OE2" Residue "A GLU 1020": "OE1" <-> "OE2" Residue "A GLU 1026": "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: 18483 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 7715 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7710 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 chain link dihedrals: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 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, 7710 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 chain link dihedrals: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 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: 7861 Chain: "C" 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 C 1 " pdbres=" C C 2 " Chain: "A" Number of atoms: 7688 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7683 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 71 Conformer: "B" Number of residues, atoms: 983, 7683 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 71 bond proxies already assigned to first conformer: 7834 Chain: "D" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1520 Unusual residues: {'GTP': 1} Classifications: {'RNA': 70, 'undetermined': 1} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 31, 'rna3p_pyr': 30} Link IDs: {'rna2p': 9, 'rna3p': 60, None: 1} Not linked: pdbres="GTP D 1 " pdbres=" C D 2 " Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AALA B 940 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA B 940 " occ=0.50 residue: pdb=" N AALA A 940 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 940 " occ=0.50 Time building chain proxies: 16.31, per 1000 atoms: 0.88 Number of scatterers: 18483 At special positions: 0 Unit cell: (202.4, 160.6, 112.2, 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 148 15.00 O 3892 8.00 N 3182 7.00 C 11199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.05 Conformation dependent library (CDL) restraints added in 4.4 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: 3694 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 11 sheets defined 41.7% alpha, 7.7% beta 33 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 8.64 Creating SS restraints... Processing helix chain 'B' and resid 74 through 88 removed outlier: 3.814A pdb=" N ILE B 78 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN B 79 " --> pdb=" O GLN B 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 83 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.996A pdb=" N PHE B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 164 " --> pdb=" O GLN B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 removed outlier: 4.121A pdb=" N LEU B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 273 removed outlier: 3.985A pdb=" N GLU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N MET B 267 " --> pdb=" O ASN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 297 removed outlier: 3.692A pdb=" N GLN B 281 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP B 285 " --> pdb=" O GLN B 281 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP B 286 " --> pdb=" O LYS B 282 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 320 removed outlier: 3.554A pdb=" N VAL B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 353 removed outlier: 4.347A pdb=" N LEU B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS B 348 " --> pdb=" O GLN B 344 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU B 353 " --> pdb=" O THR B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 417 removed outlier: 3.537A pdb=" N LYS B 405 " --> pdb=" O ILE B 401 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN B 413 " --> pdb=" O LYS B 409 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 414 " --> pdb=" O SER B 410 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 460 No H-bonds generated for 'chain 'B' and resid 457 through 460' Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 509 through 520 Proline residue: B 516 - end of helix removed outlier: 3.642A pdb=" N SER B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 590 removed outlier: 3.572A pdb=" N GLU B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 612 removed outlier: 4.282A pdb=" N LYS B 601 " --> pdb=" O MET B 597 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN B 602 " --> pdb=" O GLN B 598 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS B 606 " --> pdb=" O GLN B 602 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 607 " --> pdb=" O ARG B 603 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 610 " --> pdb=" O HIS B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 632 removed outlier: 4.118A pdb=" N GLU B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN B 631 " --> pdb=" O GLN B 627 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 632 " --> pdb=" O GLU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 648 Processing helix chain 'B' and resid 652 through 661 removed outlier: 3.676A pdb=" N ILE B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 657 " --> pdb=" O ASP B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 715 removed outlier: 3.586A pdb=" N ARG B 694 " --> pdb=" O GLU B 690 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA B 699 " --> pdb=" O LYS B 695 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 700 " --> pdb=" O GLY B 696 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 703 " --> pdb=" O ALA B 699 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 724 removed outlier: 3.913A pdb=" N ARG B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 720 through 724' Processing helix chain 'B' and resid 726 through 729 removed outlier: 4.299A pdb=" N SER B 729 " --> pdb=" O GLN B 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 726 through 729' Processing helix chain 'B' and resid 739 through 756 removed outlier: 5.064A pdb=" N ALA B 751 " --> pdb=" O GLU B 747 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 753 " --> pdb=" O THR B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 772 Proline residue: B 765 - end of helix removed outlier: 4.441A pdb=" N ALA B 771 " --> pdb=" O LYS B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 779 No H-bonds generated for 'chain 'B' and resid 777 through 779' Processing helix chain 'B' and resid 782 through 785 No H-bonds generated for 'chain 'B' and resid 782 through 785' Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 793 through 801 Processing helix chain 'B' and resid 805 through 814 removed outlier: 3.957A pdb=" N GLU B 809 " --> pdb=" O GLU B 805 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA B 810 " --> pdb=" O GLN B 806 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 847 removed outlier: 3.621A pdb=" N VAL B 832 " --> pdb=" O ASP B 828 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 833 " --> pdb=" O PRO B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 873 Processing helix chain 'B' and resid 881 through 891 removed outlier: 4.096A pdb=" N THR B 886 " --> pdb=" O THR B 882 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 887 " --> pdb=" O LYS B 883 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU B 891 " --> pdb=" O LEU B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 918 removed outlier: 3.849A pdb=" N ASP B 902 " --> pdb=" O SER B 898 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP B 918 " --> pdb=" O GLN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 929 removed outlier: 3.581A pdb=" N SER B 928 " --> pdb=" O GLU B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 952 removed outlier: 4.005A pdb=" N GLU B 946 " --> pdb=" O GLN B 942 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 948 " --> pdb=" O ALA B 944 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA B 949 " --> pdb=" O ILE B 945 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG B 952 " --> pdb=" O GLU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 970 removed outlier: 3.755A pdb=" N SER B 964 " --> pdb=" O VAL B 960 " (cutoff:3.500A) Proline residue: B 966 - end of helix removed outlier: 4.207A pdb=" N ILE B 969 " --> pdb=" O ARG B 965 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 970 " --> pdb=" O PRO B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 977 No H-bonds generated for 'chain 'B' and resid 975 through 977' Processing helix chain 'B' and resid 989 through 1003 removed outlier: 3.856A pdb=" N ASP B1003 " --> pdb=" O LEU B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1031 removed outlier: 4.963A pdb=" N GLU B1020 " --> pdb=" O ASP B1016 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU B1021 " --> pdb=" O ALA B1017 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B1022 " --> pdb=" O SER B1018 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN B1023 " --> pdb=" O LEU B1019 " (cutoff:3.500A) Proline residue: B1024 - end of helix removed outlier: 3.927A pdb=" N ASP B1027 " --> pdb=" O GLN B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1053 Processing helix chain 'A' and resid 74 through 88 removed outlier: 3.900A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 110 No H-bonds generated for 'chain 'A' and resid 107 through 110' 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 163 through 169 removed outlier: 3.629A pdb=" N SER A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 257 through 272 removed outlier: 7.199A pdb=" N GLU A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASN A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.869A pdb=" N ASP A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 318 removed outlier: 4.217A pdb=" N VAL A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 316 " --> pdb=" O HIS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.656A pdb=" N GLY A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 339 " --> pdb=" O MET A 335 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 removed outlier: 3.949A pdb=" N ILE A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 511 through 521 Proline residue: A 516 - end of helix removed outlier: 3.645A pdb=" N GLY A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 3.650A pdb=" N LYS A 590 " --> pdb=" O HIS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 604 removed outlier: 4.260A pdb=" N LYS A 601 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLN A 602 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.536A pdb=" N VAL A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 632 removed outlier: 4.516A pdb=" N ASN A 631 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 661 removed outlier: 4.193A pdb=" N THR A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 697 Processing helix chain 'A' and resid 704 through 715 removed outlier: 3.726A pdb=" N PHE A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 722 No H-bonds generated for 'chain 'A' and resid 720 through 722' Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' Processing helix chain 'A' and resid 740 through 747 removed outlier: 3.790A pdb=" N GLU A 747 " --> pdb=" O MET A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 756 No H-bonds generated for 'chain 'A' and resid 753 through 756' Processing helix chain 'A' and resid 761 through 772 Proline residue: A 765 - end of helix removed outlier: 4.932A pdb=" N ASP A 769 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 772 " --> pdb=" O ASP A 769 " (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 781 through 785 removed outlier: 3.611A pdb=" N GLU A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 781 through 785' Processing helix chain 'A' and resid 792 through 801 removed outlier: 4.474A pdb=" N TYR A 797 " --> pdb=" O MET A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Processing helix chain 'A' and resid 828 through 846 removed outlier: 4.096A pdb=" N VAL A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 873 removed outlier: 3.808A pdb=" N LEU A 868 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 884 No H-bonds generated for 'chain 'A' and resid 881 through 884' Processing helix chain 'A' and resid 901 through 919 removed outlier: 3.586A pdb=" N VAL A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN A 906 " --> pdb=" O ASP A 902 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 911 " --> pdb=" O PHE A 907 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 918 " --> pdb=" O GLN A 914 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 919 " --> pdb=" O LEU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 951 removed outlier: 3.665A pdb=" N SER A 941 " --> pdb=" O PRO A 937 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 948 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 962 removed outlier: 3.681A pdb=" N GLU A 961 " --> pdb=" O PRO A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 991 through 1002 removed outlier: 4.417A pdb=" N SER A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1017 Processing helix chain 'A' and resid 1021 through 1028 removed outlier: 3.595A pdb=" N LEU A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1054 removed outlier: 4.189A pdb=" N LEU A1049 " --> pdb=" O ARG A1045 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A1052 " --> pdb=" O LEU A1048 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 119 through 128 removed outlier: 4.057A pdb=" N THR B 208 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP B 194 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 425 through 430 removed outlier: 3.774A pdb=" N LEU B 434 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B 390 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 617 through 619 Processing sheet with id= D, first strand: chain 'B' and resid 636 through 642 removed outlier: 4.024A pdb=" N MET B 637 " --> pdb=" O ALA B 684 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 121 through 123 removed outlier: 3.614A pdb=" N GLN A 209 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 208 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP A 194 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 126 through 128 Processing sheet with id= G, first strand: chain 'A' and resid 186 through 188 Processing sheet with id= H, first strand: chain 'A' and resid 543 through 547 Processing sheet with id= I, first strand: chain 'A' and resid 451 through 453 removed outlier: 3.574A pdb=" N LEU A 452 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 498 " --> pdb=" O LEU A 452 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 617 through 619 Processing sheet with id= K, first strand: chain 'A' and resid 636 through 641 removed outlier: 3.777A pdb=" N MET A 637 " --> pdb=" O ALA A 684 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 180 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 7.95 Time building geometry restraints manager: 8.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2788 1.30 - 1.43: 5741 1.43 - 1.56: 10228 1.56 - 1.68: 294 1.68 - 1.81: 104 Bond restraints: 19155 Sorted by residual: bond pdb=" C8 GTP D 1 " pdb=" N9 GTP D 1 " ideal model delta sigma weight residual 1.370 1.197 0.173 2.00e-02 2.50e+03 7.47e+01 bond pdb=" C8 GTP C 1 " pdb=" N9 GTP C 1 " ideal model delta sigma weight residual 1.370 1.198 0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" C4 GTP D 1 " pdb=" N9 GTP D 1 " ideal model delta sigma weight residual 1.375 1.214 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O2G GTP C 1 " pdb=" PG GTP C 1 " ideal model delta sigma weight residual 1.510 1.650 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" O2G GTP D 1 " pdb=" PG GTP D 1 " ideal model delta sigma weight residual 1.510 1.648 -0.138 2.00e-02 2.50e+03 4.75e+01 ... (remaining 19150 not shown) Histogram of bond angle deviations from ideal: 99.42 - 107.26: 1400 107.26 - 115.10: 11641 115.10 - 122.95: 11957 122.95 - 130.79: 1580 130.79 - 138.63: 99 Bond angle restraints: 26677 Sorted by residual: angle pdb=" N GLY A 737 " pdb=" CA GLY A 737 " pdb=" C GLY A 737 " ideal model delta sigma weight residual 111.56 119.88 -8.32 1.01e+00 9.80e-01 6.79e+01 angle pdb=" N ARG B 965 " pdb=" CA ARG B 965 " pdb=" C ARG B 965 " ideal model delta sigma weight residual 112.75 104.00 8.75 1.36e+00 5.41e-01 4.14e+01 angle pdb=" C VAL B1034 " pdb=" N MET B1035 " pdb=" CA MET B1035 " ideal model delta sigma weight residual 120.95 113.33 7.62 1.40e+00 5.10e-01 2.96e+01 angle pdb=" C4 GTP D 1 " pdb=" N9 GTP D 1 " pdb=" C8 GTP D 1 " ideal model delta sigma weight residual 108.00 122.36 -14.36 3.00e+00 1.11e-01 2.29e+01 angle pdb=" CA ARG A 965 " pdb=" C ARG A 965 " pdb=" N PRO A 966 " ideal model delta sigma weight residual 118.44 125.95 -7.51 1.59e+00 3.96e-01 2.23e+01 ... (remaining 26672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 11199 35.69 - 71.38: 468 71.38 - 107.06: 59 107.06 - 142.75: 4 142.75 - 178.44: 4 Dihedral angle restraints: 11734 sinusoidal: 6020 harmonic: 5714 Sorted by residual: dihedral pdb=" O4' U C 19 " pdb=" C1' U C 19 " pdb=" N1 U C 19 " pdb=" C2 U C 19 " ideal model delta sinusoidal sigma weight residual 200.00 49.89 150.11 1 1.50e+01 4.44e-03 7.97e+01 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 232.00 60.14 171.86 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O5' GTP D 1 " pdb=" O3A GTP D 1 " pdb=" PA GTP D 1 " pdb=" PB GTP D 1 " ideal model delta sinusoidal sigma weight residual 274.12 95.68 178.44 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 11731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2527 0.060 - 0.119: 535 0.119 - 0.179: 68 0.179 - 0.239: 8 0.239 - 0.298: 2 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CB ILE A 970 " pdb=" CA ILE A 970 " pdb=" CG1 ILE A 970 " pdb=" CG2 ILE A 970 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB VAL B1034 " pdb=" CA VAL B1034 " pdb=" CG1 VAL B1034 " pdb=" CG2 VAL B1034 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1' U D 57 " pdb=" O4' U D 57 " pdb=" C2' U D 57 " pdb=" N1 U D 57 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 3137 not shown) Planarity restraints: 2916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 637 " -0.047 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO A 638 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 962 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C ALA A 962 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 962 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 963 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 57 " 0.028 2.00e-02 2.50e+03 1.51e-02 5.13e+00 pdb=" N1 U D 57 " -0.034 2.00e-02 2.50e+03 pdb=" C2 U D 57 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U D 57 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U D 57 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U D 57 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U D 57 " 0.006 2.00e-02 2.50e+03 pdb=" C5 U D 57 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U D 57 " -0.006 2.00e-02 2.50e+03 ... (remaining 2913 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2389 2.74 - 3.28: 17800 3.28 - 3.82: 30330 3.82 - 4.36: 35258 4.36 - 4.90: 57552 Nonbonded interactions: 143329 Sorted by model distance: nonbonded pdb=" OG1 THR B 855 " pdb=" OP1 G C 69 " model vdw 2.204 2.440 nonbonded pdb=" O LYS A1040 " pdb=" ND2 ASN A1043 " model vdw 2.205 2.520 nonbonded pdb=" NH1 ARG A 724 " pdb=" O ALA A 772 " model vdw 2.210 2.520 nonbonded pdb=" O PHE B 950 " pdb=" OG1 THR B 953 " model vdw 2.219 2.440 nonbonded pdb=" O VAL A1041 " pdb=" NH1 ARG A1045 " model vdw 2.229 2.520 ... (remaining 143324 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 and (name CA or name C or name O or name CB or name OG \ )) or resid 71 through 174 or (resid 175 and (name N or name CA or name C or na \ me O or name CB )) or resid 176 through 446 or (resid 447 through 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 or (resid 451 and (n \ ame N or name CA or name C or name O or name CB )) or resid 452 through 939 or r \ esid 941 through 944 or (resid 945 and (name N or name CA or name C or name O or \ name CB )) or resid 946 through 1068)) selection = (chain 'B' and (resid 70 through 493 or (resid 494 and (name N or name CA or nam \ e C or name O or name CB )) or resid 495 through 939 or resid 941 through 972 or \ (resid 973 through 975 and (name N or name CA or name C or name O or name CB )) \ or resid 976 through 978 or (resid 979 through 983 and (name N or name CA or na \ me C or name O or name CB )) or resid 984 through 986 or (resid 987 through 990 \ and (name N or name CA or name C or name O or name CB )) or resid 991 through 10 \ 36 or (resid 1037 through 1040 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1041 through 1047 or (resid 1048 and (name N or name CA or name \ C or name O or name CB )) or resid 1049 through 1068)) } ncs_group { reference = (chain 'C' and resid 1 through 71) 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: 6.470 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: 12.950 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 64.510 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.008 0.173 19155 Z= 0.557 Angle : 0.807 14.356 26677 Z= 0.447 Chirality : 0.049 0.298 3140 Planarity : 0.005 0.071 2916 Dihedral : 17.946 178.441 8040 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.42 % Allowed : 14.06 % Favored : 81.52 % 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: -3.24 (0.18), residues: 1964 helix: -1.92 (0.17), residues: 860 sheet: -1.19 (0.37), residues: 217 loop : -2.58 (0.18), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 298 HIS 0.005 0.001 HIS A 586 PHE 0.024 0.002 PHE A1014 TYR 0.019 0.002 TYR A 584 ARG 0.006 0.001 ARG A 432 *********************** 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 237 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 164 time to evaluate : 1.931 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: B 81 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8344 (tp) REVERT: B 267 MET cc_start: 0.9143 (mmm) cc_final: 0.8845 (mmp) REVERT: B 420 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7741 (tp) REVERT: B 488 ARG cc_start: 0.9098 (ttt180) cc_final: 0.8852 (tmm-80) REVERT: B 549 ASP cc_start: 0.9191 (t0) cc_final: 0.8939 (m-30) REVERT: B 563 ASN cc_start: 0.8434 (p0) cc_final: 0.7835 (p0) REVERT: B 659 MET cc_start: 0.8445 (mtt) cc_final: 0.8212 (ttm) REVERT: B 743 MET cc_start: 0.9420 (mmt) cc_final: 0.8361 (mmp) REVERT: B 768 LYS cc_start: 0.9560 (mtpp) cc_final: 0.9312 (mmtt) REVERT: B 775 MET cc_start: 0.9049 (tmm) cc_final: 0.7940 (ttt) REVERT: B 875 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8365 (t0) REVERT: B 947 MET cc_start: 0.9160 (tmm) cc_final: 0.8932 (tpt) REVERT: B 1034 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8204 (m) REVERT: A 81 LEU cc_start: 0.9517 (mt) cc_final: 0.9192 (tp) REVERT: A 202 MET cc_start: 0.9393 (ttp) cc_final: 0.9019 (tmm) REVERT: A 264 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8370 (tp30) REVERT: A 420 LEU cc_start: 0.9162 (mt) cc_final: 0.8864 (mm) REVERT: A 441 LEU cc_start: 0.9649 (tp) cc_final: 0.9360 (tp) REVERT: A 528 MET cc_start: 0.9368 (mtp) cc_final: 0.8942 (mtp) REVERT: A 659 MET cc_start: 0.8913 (mtm) cc_final: 0.8396 (ttm) REVERT: A 677 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8712 (tt) REVERT: A 701 LEU cc_start: 0.9132 (pp) cc_final: 0.8825 (tp) REVERT: A 714 MET cc_start: 0.9614 (ttp) cc_final: 0.9314 (ttp) REVERT: A 739 MET cc_start: 0.8753 (mmm) cc_final: 0.7985 (tpp) REVERT: A 743 MET cc_start: 0.9499 (mmm) cc_final: 0.8831 (mmm) REVERT: A 833 LEU cc_start: 0.9164 (mt) cc_final: 0.8630 (pt) REVERT: A 846 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: A 947 MET cc_start: 0.8739 (ttt) cc_final: 0.8399 (ttp) outliers start: 73 outliers final: 7 residues processed: 229 average time/residue: 0.2949 time to fit residues: 104.2926 Evaluate side-chains 103 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.997 ------------------------------------------------------------------------------- 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: 0.6980 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 138 ASN A 145 HIS A 147 GLN A 214 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A 547 HIS A 631 ASN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN A 856 ASN A 870 GLN A1031 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19155 Z= 0.152 Angle : 0.586 8.547 26677 Z= 0.295 Chirality : 0.041 0.182 3140 Planarity : 0.004 0.048 2916 Dihedral : 18.325 176.697 4365 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.85 % Favored : 95.10 % Rotamer: Outliers : 0.12 % Allowed : 2.06 % Favored : 97.82 % 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: -2.45 (0.18), residues: 1964 helix: -1.31 (0.18), residues: 855 sheet: -0.98 (0.37), residues: 220 loop : -2.03 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 530 HIS 0.008 0.001 HIS B 165 PHE 0.020 0.001 PHE A 986 TYR 0.018 0.002 TYR A 123 ARG 0.010 0.000 ARG B 426 *********************** 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 107 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 MET cc_start: 0.9341 (ppp) cc_final: 0.8963 (ppp) REVERT: B 205 MET cc_start: 0.9009 (tpp) cc_final: 0.8774 (tpt) REVERT: B 267 MET cc_start: 0.9089 (mmm) cc_final: 0.8774 (mmm) REVERT: B 549 ASP cc_start: 0.9244 (t0) cc_final: 0.8934 (m-30) REVERT: B 563 ASN cc_start: 0.8334 (p0) cc_final: 0.7667 (p0) REVERT: B 659 MET cc_start: 0.8594 (mtt) cc_final: 0.8215 (ttm) REVERT: B 743 MET cc_start: 0.9595 (mmp) cc_final: 0.9082 (mmp) REVERT: B 775 MET cc_start: 0.8936 (tmm) cc_final: 0.8053 (ptm) REVERT: B 947 MET cc_start: 0.9161 (tmm) cc_final: 0.8911 (tpt) REVERT: A 202 MET cc_start: 0.9541 (ttp) cc_final: 0.9084 (tmm) REVERT: A 205 MET cc_start: 0.8930 (tpp) cc_final: 0.8662 (tpt) REVERT: A 441 LEU cc_start: 0.9587 (tp) cc_final: 0.9352 (tp) REVERT: A 637 MET cc_start: 0.8167 (mmm) cc_final: 0.7866 (mmt) REVERT: A 659 MET cc_start: 0.9022 (mtm) cc_final: 0.8577 (ttm) REVERT: A 701 LEU cc_start: 0.9338 (pp) cc_final: 0.8990 (tp) REVERT: A 714 MET cc_start: 0.9585 (ttp) cc_final: 0.9205 (ptp) REVERT: A 739 MET cc_start: 0.8698 (mmm) cc_final: 0.8338 (tpt) REVERT: A 743 MET cc_start: 0.9525 (mmm) cc_final: 0.9220 (mmt) REVERT: A 763 MET cc_start: 0.7228 (ttp) cc_final: 0.6556 (tpt) REVERT: A 775 MET cc_start: 0.9305 (tpp) cc_final: 0.9052 (tpp) REVERT: A 833 LEU cc_start: 0.9236 (mt) cc_final: 0.8835 (pt) outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 0.3027 time to fit residues: 51.8693 Evaluate side-chains 67 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.976 ------------------------------------------------------------------------------- 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: 6.9990 chunk 59 optimal weight: 3.9990 chunk 158 optimal weight: 20.0000 chunk 129 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 170 optimal weight: 0.0170 chunk 189 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 697 ASN B 875 ASN A 75 GLN A 82 GLN A 138 ASN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 HIS A 185 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 ASN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19155 Z= 0.246 Angle : 0.666 9.431 26677 Z= 0.337 Chirality : 0.042 0.378 3140 Planarity : 0.005 0.047 2916 Dihedral : 18.331 176.870 4365 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.12 % Allowed : 2.24 % Favored : 97.64 % 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: -1.93 (0.19), residues: 1964 helix: -0.93 (0.18), residues: 868 sheet: -0.77 (0.36), residues: 212 loop : -1.69 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 186 HIS 0.012 0.002 HIS B 274 PHE 0.017 0.002 PHE A 986 TYR 0.014 0.002 TYR A 250 ARG 0.007 0.001 ARG B 426 *********************** 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 74 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9132 (ptp) cc_final: 0.8846 (pmm) REVERT: B 202 MET cc_start: 0.9331 (ppp) cc_final: 0.9108 (ppp) REVERT: B 267 MET cc_start: 0.9258 (mmm) cc_final: 0.9043 (mmm) REVERT: B 443 MET cc_start: 0.9294 (mmp) cc_final: 0.9051 (mmp) REVERT: B 549 ASP cc_start: 0.9528 (t0) cc_final: 0.9163 (m-30) REVERT: B 659 MET cc_start: 0.9040 (mtt) cc_final: 0.8213 (ttm) REVERT: B 763 MET cc_start: 0.9161 (tpt) cc_final: 0.8688 (mtt) REVERT: B 775 MET cc_start: 0.8969 (tmm) cc_final: 0.8565 (tmm) REVERT: B 947 MET cc_start: 0.9299 (tmm) cc_final: 0.9069 (tmm) REVERT: A 202 MET cc_start: 0.9663 (ttp) cc_final: 0.8975 (tmm) REVERT: A 205 MET cc_start: 0.9253 (tpp) cc_final: 0.8846 (tpp) REVERT: A 441 LEU cc_start: 0.9596 (tp) cc_final: 0.9348 (tp) REVERT: A 637 MET cc_start: 0.8524 (mmm) cc_final: 0.8077 (mpp) REVERT: A 659 MET cc_start: 0.9357 (mtm) cc_final: 0.8688 (ttm) REVERT: A 701 LEU cc_start: 0.9752 (pp) cc_final: 0.9437 (tp) REVERT: A 714 MET cc_start: 0.9646 (ttp) cc_final: 0.9244 (ptp) REVERT: A 743 MET cc_start: 0.9629 (mmm) cc_final: 0.9406 (mmm) REVERT: A 763 MET cc_start: 0.7917 (ttp) cc_final: 0.7248 (tpt) REVERT: A 775 MET cc_start: 0.9436 (tpp) cc_final: 0.9084 (tpp) REVERT: A 833 LEU cc_start: 0.9404 (mt) cc_final: 0.8860 (pt) REVERT: A 947 MET cc_start: 0.8664 (ttm) cc_final: 0.8176 (tpp) outliers start: 2 outliers final: 0 residues processed: 74 average time/residue: 0.2821 time to fit residues: 35.2056 Evaluate side-chains 60 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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: 2.9990 chunk 143 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 128 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 138 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19155 Z= 0.159 Angle : 0.541 7.944 26677 Z= 0.271 Chirality : 0.039 0.161 3140 Planarity : 0.004 0.044 2916 Dihedral : 18.143 178.553 4365 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.06 % Allowed : 1.15 % Favored : 98.79 % 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: -1.56 (0.19), residues: 1964 helix: -0.54 (0.18), residues: 877 sheet: -0.98 (0.35), residues: 227 loop : -1.48 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 186 HIS 0.005 0.001 HIS A 244 PHE 0.015 0.001 PHE A 846 TYR 0.015 0.001 TYR A 705 ARG 0.007 0.000 ARG B 426 *********************** 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 72 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9097 (ptp) cc_final: 0.8778 (pmm) REVERT: B 267 MET cc_start: 0.9345 (mmm) cc_final: 0.9060 (mmm) REVERT: B 549 ASP cc_start: 0.9553 (t0) cc_final: 0.9124 (m-30) REVERT: B 637 MET cc_start: 0.9564 (mmp) cc_final: 0.9253 (mmm) REVERT: B 659 MET cc_start: 0.9000 (mtt) cc_final: 0.8205 (ttm) REVERT: B 763 MET cc_start: 0.9233 (tpt) cc_final: 0.8805 (mtt) REVERT: B 775 MET cc_start: 0.8923 (tmm) cc_final: 0.8359 (tmm) REVERT: B 947 MET cc_start: 0.9314 (tmm) cc_final: 0.9087 (tmm) REVERT: A 202 MET cc_start: 0.9633 (ttp) cc_final: 0.9219 (tmm) REVERT: A 441 LEU cc_start: 0.9578 (tp) cc_final: 0.9346 (tp) REVERT: A 446 MET cc_start: 0.8867 (mpp) cc_final: 0.8522 (tpp) REVERT: A 637 MET cc_start: 0.8580 (mmm) cc_final: 0.8359 (mmt) REVERT: A 659 MET cc_start: 0.9356 (mtm) cc_final: 0.8769 (ttm) REVERT: A 714 MET cc_start: 0.9697 (ttp) cc_final: 0.9300 (ptp) REVERT: A 739 MET cc_start: 0.8839 (tpt) cc_final: 0.8519 (tpt) REVERT: A 763 MET cc_start: 0.7922 (ttp) cc_final: 0.7335 (tpt) REVERT: A 775 MET cc_start: 0.9374 (tpp) cc_final: 0.9060 (tpp) REVERT: A 833 LEU cc_start: 0.9345 (mt) cc_final: 0.8835 (pt) REVERT: A 947 MET cc_start: 0.8748 (ttm) cc_final: 0.8366 (tpp) REVERT: A 1035 MET cc_start: 0.8659 (mpp) cc_final: 0.8148 (mpp) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.2808 time to fit residues: 33.4985 Evaluate side-chains 60 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.873 ------------------------------------------------------------------------------- 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: 0.0000 chunk 115 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 51 optimal weight: 0.0670 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN B 341 GLN B 442 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 138 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 ASN A 748 ASN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19155 Z= 0.170 Angle : 0.547 7.853 26677 Z= 0.274 Chirality : 0.039 0.180 3140 Planarity : 0.004 0.044 2916 Dihedral : 18.105 178.009 4365 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.06 % Allowed : 1.09 % Favored : 98.85 % 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: 883 sheet: -0.72 (0.36), residues: 223 loop : -1.35 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 186 HIS 0.007 0.001 HIS A 244 PHE 0.015 0.001 PHE A 986 TYR 0.022 0.002 TYR A 705 ARG 0.007 0.000 ARG A 538 *********************** 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 68 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.8506 (mpp) cc_final: 0.8281 (mpp) REVERT: B 105 MET cc_start: 0.9031 (ptp) cc_final: 0.8632 (pmm) REVERT: B 267 MET cc_start: 0.9367 (mmm) cc_final: 0.8895 (mmm) REVERT: B 549 ASP cc_start: 0.9565 (t0) cc_final: 0.9166 (m-30) REVERT: B 637 MET cc_start: 0.9625 (mmp) cc_final: 0.9303 (mmm) REVERT: B 659 MET cc_start: 0.9080 (mtt) cc_final: 0.8240 (ttm) REVERT: B 739 MET cc_start: 0.9119 (tpt) cc_final: 0.8479 (tpp) REVERT: B 743 MET cc_start: 0.9522 (mmp) cc_final: 0.9088 (mmt) REVERT: B 763 MET cc_start: 0.9282 (tpt) cc_final: 0.8727 (mtm) REVERT: B 947 MET cc_start: 0.9407 (tmm) cc_final: 0.9186 (tmm) REVERT: A 202 MET cc_start: 0.9595 (ttp) cc_final: 0.9159 (tmm) REVERT: A 441 LEU cc_start: 0.9558 (tp) cc_final: 0.9310 (tp) REVERT: A 446 MET cc_start: 0.8863 (mpp) cc_final: 0.8580 (tpp) REVERT: A 714 MET cc_start: 0.9710 (ttp) cc_final: 0.9319 (ptp) REVERT: A 739 MET cc_start: 0.8899 (tpt) cc_final: 0.7916 (tpt) REVERT: A 743 MET cc_start: 0.9704 (mmm) cc_final: 0.8939 (mmm) REVERT: A 763 MET cc_start: 0.8268 (ttp) cc_final: 0.7766 (tpp) REVERT: A 833 LEU cc_start: 0.9365 (mt) cc_final: 0.8758 (pt) REVERT: A 947 MET cc_start: 0.8972 (ttm) cc_final: 0.8565 (tpp) REVERT: A 1035 MET cc_start: 0.8474 (mpp) cc_final: 0.8154 (mpp) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.3030 time to fit residues: 33.3779 Evaluate side-chains 57 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.936 ------------------------------------------------------------------------------- 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: 0.0020 chunk 182 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 138 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19155 Z= 0.147 Angle : 0.523 9.023 26677 Z= 0.258 Chirality : 0.039 0.158 3140 Planarity : 0.004 0.047 2916 Dihedral : 18.065 178.420 4365 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.06 % Allowed : 1.03 % Favored : 98.91 % 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: -0.97 (0.19), residues: 1964 helix: 0.03 (0.18), residues: 891 sheet: -0.85 (0.36), residues: 231 loop : -1.23 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 186 HIS 0.005 0.001 HIS A 244 PHE 0.027 0.001 PHE A 666 TYR 0.010 0.001 TYR B 212 ARG 0.005 0.000 ARG B 426 *********************** 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 66 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.8463 (mpp) cc_final: 0.8231 (mpp) REVERT: B 105 MET cc_start: 0.8939 (ptp) cc_final: 0.8488 (pmm) REVERT: B 267 MET cc_start: 0.9434 (mmm) cc_final: 0.9017 (mmm) REVERT: B 549 ASP cc_start: 0.9553 (t0) cc_final: 0.9148 (m-30) REVERT: B 637 MET cc_start: 0.9519 (mmp) cc_final: 0.9181 (mmt) REVERT: B 659 MET cc_start: 0.9067 (mtt) cc_final: 0.8273 (ttm) REVERT: B 739 MET cc_start: 0.9109 (tpt) cc_final: 0.8727 (tpp) REVERT: B 743 MET cc_start: 0.9543 (mmp) cc_final: 0.9279 (mmt) REVERT: B 763 MET cc_start: 0.9331 (tpt) cc_final: 0.8813 (mtm) REVERT: B 775 MET cc_start: 0.8848 (tmm) cc_final: 0.8244 (tmm) REVERT: A 202 MET cc_start: 0.9572 (ttp) cc_final: 0.9165 (tmm) REVERT: A 441 LEU cc_start: 0.9534 (tp) cc_final: 0.9285 (tp) REVERT: A 446 MET cc_start: 0.8915 (mpp) cc_final: 0.8678 (tpp) REVERT: A 659 MET cc_start: 0.9048 (ttp) cc_final: 0.8228 (tmm) REVERT: A 714 MET cc_start: 0.9696 (ttp) cc_final: 0.9302 (ptp) REVERT: A 739 MET cc_start: 0.8937 (tpt) cc_final: 0.8634 (tpt) REVERT: A 743 MET cc_start: 0.9705 (mmm) cc_final: 0.9463 (mtp) REVERT: A 763 MET cc_start: 0.8073 (ttp) cc_final: 0.7674 (tpp) REVERT: A 775 MET cc_start: 0.9340 (mmp) cc_final: 0.9080 (tpp) REVERT: A 833 LEU cc_start: 0.9335 (mt) cc_final: 0.8723 (pt) REVERT: A 947 MET cc_start: 0.9038 (ttm) cc_final: 0.8596 (tpp) REVERT: A 1035 MET cc_start: 0.8466 (mpp) cc_final: 0.8018 (mpp) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.2898 time to fit residues: 31.8779 Evaluate side-chains 56 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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: 8.9990 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 123 optimal weight: 0.0870 chunk 93 optimal weight: 8.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 215 GLN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 138 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19155 Z= 0.121 Angle : 0.504 9.212 26677 Z= 0.245 Chirality : 0.038 0.157 3140 Planarity : 0.003 0.048 2916 Dihedral : 17.927 178.274 4365 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.06 % Allowed : 0.67 % Favored : 99.27 % 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: -0.68 (0.19), residues: 1964 helix: 0.32 (0.18), residues: 887 sheet: -0.60 (0.36), residues: 226 loop : -1.16 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 186 HIS 0.004 0.001 HIS A 244 PHE 0.009 0.001 PHE B 284 TYR 0.015 0.001 TYR B 135 ARG 0.005 0.000 ARG B 426 *********************** 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 66 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8942 (ptp) cc_final: 0.8566 (pmm) REVERT: B 237 MET cc_start: 0.9452 (ptm) cc_final: 0.8456 (ttp) REVERT: B 267 MET cc_start: 0.9487 (mmm) cc_final: 0.9240 (mmp) REVERT: B 549 ASP cc_start: 0.9525 (t0) cc_final: 0.9143 (m-30) REVERT: B 637 MET cc_start: 0.9558 (mmp) cc_final: 0.9266 (mmm) REVERT: B 659 MET cc_start: 0.9036 (mtt) cc_final: 0.8255 (ttm) REVERT: B 739 MET cc_start: 0.9095 (tpt) cc_final: 0.8776 (tpp) REVERT: B 743 MET cc_start: 0.9536 (mmp) cc_final: 0.9282 (mmt) REVERT: B 763 MET cc_start: 0.9327 (tpt) cc_final: 0.8856 (mtm) REVERT: B 775 MET cc_start: 0.8980 (tmm) cc_final: 0.8494 (tmm) REVERT: A 202 MET cc_start: 0.9570 (ttp) cc_final: 0.9237 (tmm) REVERT: A 441 LEU cc_start: 0.9518 (tp) cc_final: 0.9271 (tp) REVERT: A 446 MET cc_start: 0.8947 (mpp) cc_final: 0.8729 (tpp) REVERT: A 637 MET cc_start: 0.9331 (mmp) cc_final: 0.8930 (mmm) REVERT: A 659 MET cc_start: 0.9137 (ttp) cc_final: 0.8252 (tmm) REVERT: A 714 MET cc_start: 0.9705 (ttp) cc_final: 0.9324 (ptp) REVERT: A 739 MET cc_start: 0.8944 (tpt) cc_final: 0.8612 (tpt) REVERT: A 763 MET cc_start: 0.7980 (ttp) cc_final: 0.7746 (tpp) REVERT: A 833 LEU cc_start: 0.9287 (mt) cc_final: 0.8685 (pt) REVERT: A 947 MET cc_start: 0.9011 (ttm) cc_final: 0.8590 (tpp) REVERT: A 1035 MET cc_start: 0.8353 (mpp) cc_final: 0.7991 (mpp) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.2958 time to fit residues: 32.4810 Evaluate side-chains 57 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.979 ------------------------------------------------------------------------------- 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: 0.5980 chunk 120 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 184 optimal weight: 7.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 631 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19155 Z= 0.141 Angle : 0.516 9.607 26677 Z= 0.253 Chirality : 0.038 0.149 3140 Planarity : 0.003 0.047 2916 Dihedral : 17.956 177.959 4365 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -0.52 (0.20), residues: 1964 helix: 0.47 (0.18), residues: 879 sheet: -0.58 (0.36), residues: 226 loop : -1.06 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 119 HIS 0.003 0.001 HIS A 244 PHE 0.011 0.001 PHE B 284 TYR 0.011 0.001 TYR B 212 ARG 0.004 0.000 ARG B 426 *********************** 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 65 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 MET cc_start: 0.9506 (ptm) cc_final: 0.8450 (ttp) REVERT: B 267 MET cc_start: 0.9555 (mmm) cc_final: 0.9315 (mmp) REVERT: B 549 ASP cc_start: 0.9541 (t0) cc_final: 0.9156 (m-30) REVERT: B 637 MET cc_start: 0.9511 (mmp) cc_final: 0.9170 (mmt) REVERT: B 659 MET cc_start: 0.9066 (mtt) cc_final: 0.8301 (ttm) REVERT: B 714 MET cc_start: 0.8688 (tmm) cc_final: 0.8378 (tmm) REVERT: B 763 MET cc_start: 0.9346 (tpt) cc_final: 0.8890 (mtm) REVERT: B 775 MET cc_start: 0.8965 (tmm) cc_final: 0.8377 (tmm) REVERT: A 202 MET cc_start: 0.9603 (ttp) cc_final: 0.9187 (tmm) REVERT: A 441 LEU cc_start: 0.9509 (tp) cc_final: 0.9255 (tp) REVERT: A 446 MET cc_start: 0.8977 (mpp) cc_final: 0.8731 (tpp) REVERT: A 637 MET cc_start: 0.9295 (mmp) cc_final: 0.8903 (mmm) REVERT: A 659 MET cc_start: 0.9100 (ttp) cc_final: 0.8264 (tmm) REVERT: A 714 MET cc_start: 0.9695 (ttp) cc_final: 0.9309 (ptp) REVERT: A 739 MET cc_start: 0.8957 (tpt) cc_final: 0.8392 (tpt) REVERT: A 743 MET cc_start: 0.9773 (mmm) cc_final: 0.9061 (mmp) REVERT: A 763 MET cc_start: 0.8153 (ttp) cc_final: 0.7896 (tpp) REVERT: A 833 LEU cc_start: 0.9330 (mt) cc_final: 0.8717 (pt) REVERT: A 947 MET cc_start: 0.9038 (ttm) cc_final: 0.8653 (tpp) REVERT: A 1035 MET cc_start: 0.8379 (mpp) cc_final: 0.7973 (mpp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2762 time to fit residues: 30.1284 Evaluate side-chains 56 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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: 10.0000 chunk 176 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 187 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 82 GLN A 138 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.6705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19155 Z= 0.140 Angle : 0.517 9.681 26677 Z= 0.253 Chirality : 0.038 0.149 3140 Planarity : 0.004 0.046 2916 Dihedral : 17.960 178.236 4365 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.06 % Allowed : 0.42 % Favored : 99.52 % 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: -0.39 (0.20), residues: 1964 helix: 0.64 (0.19), residues: 868 sheet: -0.57 (0.36), residues: 226 loop : -1.04 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 186 HIS 0.004 0.001 HIS A 244 PHE 0.011 0.001 PHE B 260 TYR 0.020 0.001 TYR A 705 ARG 0.008 0.000 ARG A 234 *********************** 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 64 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.8503 (mpp) cc_final: 0.8228 (mmp) REVERT: B 105 MET cc_start: 0.9211 (ptp) cc_final: 0.8848 (pmm) REVERT: B 237 MET cc_start: 0.9526 (ptm) cc_final: 0.8505 (ttp) REVERT: B 267 MET cc_start: 0.9606 (mmm) cc_final: 0.9356 (mmp) REVERT: B 549 ASP cc_start: 0.9530 (t0) cc_final: 0.9156 (m-30) REVERT: B 637 MET cc_start: 0.9541 (mmp) cc_final: 0.9154 (mmt) REVERT: B 659 MET cc_start: 0.9081 (mtt) cc_final: 0.8325 (ttm) REVERT: B 714 MET cc_start: 0.8709 (tmm) cc_final: 0.8402 (tmm) REVERT: B 739 MET cc_start: 0.9207 (tpt) cc_final: 0.8726 (tpp) REVERT: B 743 MET cc_start: 0.9559 (mmp) cc_final: 0.9276 (mmt) REVERT: B 763 MET cc_start: 0.9384 (tpt) cc_final: 0.8945 (mtm) REVERT: B 775 MET cc_start: 0.9015 (tmm) cc_final: 0.8652 (tmm) REVERT: A 202 MET cc_start: 0.9578 (ttp) cc_final: 0.9180 (tmm) REVERT: A 441 LEU cc_start: 0.9517 (tp) cc_final: 0.9270 (tp) REVERT: A 446 MET cc_start: 0.9007 (mpp) cc_final: 0.8694 (tpp) REVERT: A 597 MET cc_start: 0.9310 (ppp) cc_final: 0.9005 (ppp) REVERT: A 637 MET cc_start: 0.9289 (mmp) cc_final: 0.8880 (mmm) REVERT: A 659 MET cc_start: 0.9103 (ttp) cc_final: 0.8279 (tmm) REVERT: A 714 MET cc_start: 0.9691 (ttp) cc_final: 0.9286 (ptp) REVERT: A 739 MET cc_start: 0.8980 (tpt) cc_final: 0.8692 (tpt) REVERT: A 775 MET cc_start: 0.9489 (tpp) cc_final: 0.9194 (tpp) REVERT: A 833 LEU cc_start: 0.9342 (mt) cc_final: 0.8742 (pt) REVERT: A 947 MET cc_start: 0.9062 (ttm) cc_final: 0.8700 (tpp) REVERT: A 1035 MET cc_start: 0.8425 (mpp) cc_final: 0.8064 (mpp) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.2988 time to fit residues: 32.0770 Evaluate side-chains 56 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 2.004 ------------------------------------------------------------------------------- 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: 9.9990 chunk 121 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 209 optimal weight: 20.0000 chunk 192 optimal weight: 1.9990 chunk 166 optimal weight: 0.2980 chunk 17 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 20.0000 chunk 132 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 442 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 82 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.6849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19155 Z= 0.124 Angle : 0.515 9.978 26677 Z= 0.250 Chirality : 0.038 0.153 3140 Planarity : 0.003 0.047 2916 Dihedral : 17.919 178.103 4365 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.30 (0.20), residues: 1964 helix: 0.68 (0.19), residues: 873 sheet: -0.48 (0.36), residues: 225 loop : -0.97 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 186 HIS 0.003 0.001 HIS A 244 PHE 0.010 0.001 PHE B 284 TYR 0.013 0.001 TYR B 271 ARG 0.004 0.000 ARG B 426 ********************** 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 64 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.8596 (mpp) cc_final: 0.8378 (mmp) REVERT: B 105 MET cc_start: 0.9123 (ptp) cc_final: 0.8669 (pmm) REVERT: B 237 MET cc_start: 0.9517 (ptm) cc_final: 0.8336 (ttp) REVERT: B 267 MET cc_start: 0.9626 (mmm) cc_final: 0.9323 (mmp) REVERT: B 549 ASP cc_start: 0.9526 (t0) cc_final: 0.9095 (m-30) REVERT: B 637 MET cc_start: 0.9542 (mmp) cc_final: 0.9163 (mmt) REVERT: B 659 MET cc_start: 0.9058 (mtt) cc_final: 0.8294 (ttm) REVERT: B 714 MET cc_start: 0.8681 (tmm) cc_final: 0.8383 (tmm) REVERT: B 739 MET cc_start: 0.9220 (tpt) cc_final: 0.8665 (tpp) REVERT: B 743 MET cc_start: 0.9535 (mmp) cc_final: 0.9197 (mmt) REVERT: B 763 MET cc_start: 0.9386 (tpt) cc_final: 0.8976 (mtm) REVERT: B 775 MET cc_start: 0.8905 (tmm) cc_final: 0.8609 (tmm) REVERT: A 202 MET cc_start: 0.9580 (ttp) cc_final: 0.9183 (tmm) REVERT: A 237 MET cc_start: 0.9501 (ptp) cc_final: 0.9188 (ptt) REVERT: A 441 LEU cc_start: 0.9530 (tp) cc_final: 0.9281 (tp) REVERT: A 446 MET cc_start: 0.9004 (mpp) cc_final: 0.8681 (tpp) REVERT: A 597 MET cc_start: 0.9304 (ppp) cc_final: 0.9018 (ppp) REVERT: A 637 MET cc_start: 0.9273 (mmp) cc_final: 0.8871 (mmm) REVERT: A 659 MET cc_start: 0.9052 (ttp) cc_final: 0.8750 (ttp) REVERT: A 714 MET cc_start: 0.9686 (ttp) cc_final: 0.9306 (ptp) REVERT: A 739 MET cc_start: 0.8965 (tpt) cc_final: 0.8523 (tpt) REVERT: A 743 MET cc_start: 0.9806 (mmm) cc_final: 0.9026 (mmp) REVERT: A 763 MET cc_start: 0.8865 (tpp) cc_final: 0.8599 (ttt) REVERT: A 833 LEU cc_start: 0.9332 (mt) cc_final: 0.8726 (pt) REVERT: A 947 MET cc_start: 0.9071 (ttm) cc_final: 0.8714 (tpp) REVERT: A 1035 MET cc_start: 0.8445 (mpp) cc_final: 0.8096 (mpp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3024 time to fit residues: 32.4412 Evaluate side-chains 57 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.931 ------------------------------------------------------------------------------- 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: 0.3980 chunk 51 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 166 optimal weight: 5.9990 chunk 69 optimal weight: 0.0000 chunk 171 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 442 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 82 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.035077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.025290 restraints weight = 236246.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.026021 restraints weight = 141901.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.026532 restraints weight = 98408.903| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19155 Z= 0.129 Angle : 0.512 9.543 26677 Z= 0.248 Chirality : 0.038 0.151 3140 Planarity : 0.003 0.046 2916 Dihedral : 17.910 177.964 4365 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.23 (0.20), residues: 1964 helix: 0.72 (0.19), residues: 877 sheet: -0.42 (0.36), residues: 225 loop : -0.93 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 119 HIS 0.006 0.001 HIS B 547 PHE 0.010 0.001 PHE B 284 TYR 0.011 0.001 TYR B 212 ARG 0.004 0.000 ARG B 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2940.59 seconds wall clock time: 54 minutes 28.25 seconds (3268.25 seconds total)