Starting phenix.real_space_refine on Sat Mar 16 12:09:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liw_23387/03_2024/7liw_23387_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liw_23387/03_2024/7liw_23387.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liw_23387/03_2024/7liw_23387_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liw_23387/03_2024/7liw_23387_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liw_23387/03_2024/7liw_23387_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liw_23387/03_2024/7liw_23387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liw_23387/03_2024/7liw_23387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liw_23387/03_2024/7liw_23387_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liw_23387/03_2024/7liw_23387_updated.pdb" } resolution = 2.85 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= -0.007 sd= 0.199 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 6 5.49 5 S 101 5.16 5 C 9333 2.51 5 N 2481 2.21 5 O 2677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 891": "OE1" <-> "OE2" Residue "A ARG 976": "NH1" <-> "NH2" Residue "A ARG 986": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1045": "NH1" <-> "NH2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A GLU 1097": "OE1" <-> "OE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B ARG 653": "NH1" <-> "NH2" Residue "B ARG 676": "NH1" <-> "NH2" Residue "B ARG 691": "NH1" <-> "NH2" Residue "B ARG 729": "NH1" <-> "NH2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "B GLU 781": "OE1" <-> "OE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "B GLU 847": "OE1" <-> "OE2" Residue "B GLU 851": "OE1" <-> "OE2" Residue "B ARG 986": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1045": "NH1" <-> "NH2" Residue "B GLU 1050": "OE1" <-> "OE2" Residue "B ARG 1085": "NH1" <-> "NH2" Residue "B GLU 1097": "OE1" <-> "OE2" Residue "C ARG 986": "NH1" <-> "NH2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C GLU 1009": "OE1" <-> "OE2" Residue "C GLU 1011": "OE1" <-> "OE2" Residue "C ARG 1045": "NH1" <-> "NH2" Residue "C GLU 1050": "OE1" <-> "OE2" Residue "C ARG 1085": "NH1" <-> "NH2" Residue "C GLU 1097": "OE1" <-> "OE2" Residue "D GLU 891": "OE1" <-> "OE2" Residue "D ARG 986": "NH1" <-> "NH2" Residue "D ARG 995": "NH1" <-> "NH2" Residue "D ARG 1045": "NH1" <-> "NH2" Residue "D ARG 1085": "NH1" <-> "NH2" Residue "D GLU 1097": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14598 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2163 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 8011 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1034, 7994 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 982} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 1034, 7994 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 982} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 8153 Chain: "C" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2166 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2166 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'ADP': 1, 'COA': 1, 'Y2A': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 11.72, per 1000 atoms: 0.80 Number of scatterers: 14598 At special positions: 0 Unit cell: (93.96, 100.92, 140.07, 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 101 16.00 P 6 15.00 O 2677 8.00 N 2481 7.00 C 9333 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=0, symmetry=0 Time building additional restraints: 5.40 Conformation dependent library (CDL) restraints added in 4.1 seconds 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 8 sheets defined 46.9% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.28 Creating SS restraints... Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 859 through 864 removed outlier: 3.631A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 876 removed outlier: 3.534A pdb=" N LEU A 875 " --> pdb=" O GLY A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 905 through 915 Processing helix chain 'A' and resid 920 through 930 removed outlier: 3.697A pdb=" N GLY A 927 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 951 Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 985 through 997 Processing helix chain 'A' and resid 1002 through 1016 removed outlier: 4.126A pdb=" N SER A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1038 removed outlier: 3.600A pdb=" N VAL A1031 " --> pdb=" O GLY A1027 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1034 " --> pdb=" O GLY A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1054 removed outlier: 3.577A pdb=" N TYR A1051 " --> pdb=" O GLU A1047 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A1052 " --> pdb=" O ALA A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1078 removed outlier: 3.633A pdb=" N PHE A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A1071 " --> pdb=" O MET A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1090 No H-bonds generated for 'chain 'A' and resid 1088 through 1090' Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 78 through 86 removed outlier: 3.846A pdb=" N LYS B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 168 removed outlier: 3.637A pdb=" N LYS B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 194 removed outlier: 3.684A pdb=" N LYS B 178 " --> pdb=" O GLU B 175 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLU B 179 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B 180 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 181 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA B 182 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER B 183 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE B 185 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 186 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN B 190 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP B 194 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 removed outlier: 3.641A pdb=" N ASP B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR B 227 " --> pdb=" O THR B 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 227' Processing helix chain 'B' and resid 230 through 233 No H-bonds generated for 'chain 'B' and resid 230 through 233' Processing helix chain 'B' and resid 248 through 259 removed outlier: 3.538A pdb=" N ALA B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.522A pdb=" N ARG B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.665A pdb=" N GLU B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.811A pdb=" N GLY B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 419 removed outlier: 4.270A pdb=" N ILE B 414 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 415 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET B 417 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 419 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 518 Processing helix chain 'B' and resid 556 through 562 Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.575A pdb=" N THR B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 616 removed outlier: 3.610A pdb=" N LYS B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 648 Processing helix chain 'B' and resid 665 through 677 Processing helix chain 'B' and resid 698 through 705 removed outlier: 3.505A pdb=" N LEU B 702 " --> pdb=" O MET B 698 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG B 703 " --> pdb=" O ASP B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 732 Processing helix chain 'B' and resid 747 through 750 removed outlier: 3.627A pdb=" N THR B 750 " --> pdb=" O THR B 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 747 through 750' Processing helix chain 'B' and resid 772 through 781 removed outlier: 3.783A pdb=" N LYS B 780 " --> pdb=" O ASN B 776 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU B 781 " --> pdb=" O GLN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 806 removed outlier: 5.151A pdb=" N GLY B 794 " --> pdb=" O ASP B 791 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 795 " --> pdb=" O GLU B 792 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 797 " --> pdb=" O GLY B 794 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN B 798 " --> pdb=" O GLU B 795 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B 799 " --> pdb=" O ILE B 796 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 800 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU B 802 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL B 805 " --> pdb=" O GLU B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 859 through 864 removed outlier: 3.533A pdb=" N PHE B 863 " --> pdb=" O ILE B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 876 Processing helix chain 'B' and resid 884 through 896 Processing helix chain 'B' and resid 905 through 915 Processing helix chain 'B' and resid 920 through 930 removed outlier: 3.507A pdb=" N GLY B 927 " --> pdb=" O SER B 923 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 951 removed outlier: 3.710A pdb=" N ALA B 943 " --> pdb=" O LEU B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 965 Processing helix chain 'B' and resid 985 through 997 Processing helix chain 'B' and resid 1002 through 1016 removed outlier: 3.503A pdb=" N GLU B1009 " --> pdb=" O ASP B1005 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B1013 " --> pdb=" O GLU B1009 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER B1016 " --> pdb=" O LYS B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1039 removed outlier: 3.686A pdb=" N VAL B1031 " --> pdb=" O GLY B1027 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B1035 " --> pdb=" O VAL B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1054 removed outlier: 3.675A pdb=" N GLU B1050 " --> pdb=" O GLU B1046 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B1052 " --> pdb=" O ALA B1048 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1078 removed outlier: 3.580A pdb=" N PHE B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1090 No H-bonds generated for 'chain 'B' and resid 1088 through 1090' Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 859 through 864 removed outlier: 3.596A pdb=" N PHE C 863 " --> pdb=" O ILE C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 877 Processing helix chain 'C' and resid 884 through 896 Processing helix chain 'C' and resid 905 through 915 removed outlier: 3.507A pdb=" N ASN C 909 " --> pdb=" O SER C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 930 removed outlier: 3.553A pdb=" N GLY C 927 " --> pdb=" O SER C 923 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 951 removed outlier: 3.638A pdb=" N ALA C 943 " --> pdb=" O LEU C 939 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 965 removed outlier: 3.599A pdb=" N LYS C 962 " --> pdb=" O GLU C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 997 Processing helix chain 'C' and resid 1002 through 1015 removed outlier: 3.545A pdb=" N LYS C1012 " --> pdb=" O LEU C1008 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C1013 " --> pdb=" O GLU C1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1037 removed outlier: 3.661A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C1034 " --> pdb=" O GLY C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1054 removed outlier: 3.670A pdb=" N ILE C1052 " --> pdb=" O ALA C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1078 removed outlier: 3.597A pdb=" N PHE C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 830 Processing helix chain 'D' and resid 859 through 864 removed outlier: 3.596A pdb=" N PHE D 863 " --> pdb=" O ILE D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 878 Processing helix chain 'D' and resid 884 through 896 Processing helix chain 'D' and resid 905 through 915 removed outlier: 3.639A pdb=" N ASN D 909 " --> pdb=" O SER D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 930 removed outlier: 3.581A pdb=" N GLY D 927 " --> pdb=" O SER D 923 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR D 930 " --> pdb=" O SER D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 951 removed outlier: 3.578A pdb=" N ALA D 943 " --> pdb=" O LEU D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 965 Processing helix chain 'D' and resid 985 through 997 Processing helix chain 'D' and resid 1002 through 1014 removed outlier: 3.606A pdb=" N ILE D1013 " --> pdb=" O GLU D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1025 through 1038 removed outlier: 3.540A pdb=" N VAL D1034 " --> pdb=" O GLY D1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 1045 through 1054 removed outlier: 3.753A pdb=" N ILE D1052 " --> pdb=" O ALA D1048 " (cutoff:3.500A) Processing helix chain 'D' and resid 1056 through 1078 removed outlier: 3.515A pdb=" N ILE D1060 " --> pdb=" O ALA D1056 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1088 through 1090 No H-bonds generated for 'chain 'D' and resid 1088 through 1090' Processing sheet with id= A, first strand: chain 'B' and resid 3 through 6 removed outlier: 4.697A pdb=" N ALA B 219 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR B 198 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 31 through 34 Processing sheet with id= C, first strand: chain 'B' and resid 92 through 95 removed outlier: 3.772A pdb=" N ALA B 98 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 205 through 207 Processing sheet with id= E, first strand: chain 'B' and resid 263 through 268 Processing sheet with id= F, first strand: chain 'B' and resid 275 through 277 removed outlier: 6.148A pdb=" N ILE B 337 " --> pdb=" O TRP B 276 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 537 through 543 removed outlier: 8.439A pdb=" N ALA B 527 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ALA B 499 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N MET B 529 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B 501 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE B 500 " --> pdb=" O ASP B 567 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 569 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TRP B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN B 571 " --> pdb=" O TRP B 502 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR B 593 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASN B 571 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 595 " --> pdb=" O ASN B 571 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR B 619 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE B 596 " --> pdb=" O THR B 619 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 621 " --> pdb=" O ILE B 596 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 739 through 744 removed outlier: 7.384A pdb=" N TYR B 659 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY B 684 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N SER B 661 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA B 686 " --> pdb=" O SER B 661 " (cutoff:3.500A) 541 hydrogen bonds defined for protein. 1554 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.71: 14743 1.71 - 2.25: 170 2.25 - 2.79: 0 2.79 - 3.33: 0 3.33 - 3.87: 2 Bond restraints: 14915 Sorted by residual: bond pdb=" AO6 COA B2002 " pdb=" AP2 COA B2002 " ideal model delta sigma weight residual 1.610 3.871 -2.261 2.00e-02 2.50e+03 1.28e+04 bond pdb=" AP1 COA B2002 " pdb="AO5* COA B2002 " ideal model delta sigma weight residual 1.610 3.736 -2.126 2.00e-02 2.50e+03 1.13e+04 bond pdb=" PC9 COA B2002 " pdb=" PO9 COA B2002 " ideal model delta sigma weight residual 1.410 1.191 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C1' ADP B2001 " pdb=" C2' ADP B2001 " ideal model delta sigma weight residual 1.306 1.518 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C1' ADP B2001 " pdb=" O4' ADP B2001 " ideal model delta sigma weight residual 1.615 1.429 0.186 2.00e-02 2.50e+03 8.67e+01 ... (remaining 14910 not shown) Histogram of bond angle deviations from ideal: 20.83 - 44.14: 2 44.14 - 67.45: 0 67.45 - 90.75: 0 90.75 - 114.06: 8865 114.06 - 137.36: 11305 Bond angle restraints: 20172 Sorted by residual: angle pdb=" AO3 COA B2002 " pdb=" AP2 COA B2002 " pdb=" AO6 COA B2002 " ideal model delta sigma weight residual 102.60 20.83 81.77 3.00e+00 1.11e-01 7.43e+02 angle pdb=" AO3 COA B2002 " pdb=" AP1 COA B2002 " pdb="AO5* COA B2002 " ideal model delta sigma weight residual 102.60 28.53 74.07 3.00e+00 1.11e-01 6.10e+02 angle pdb=" AP1 COA B2002 " pdb="AO5* COA B2002 " pdb="AC5* COA B2002 " ideal model delta sigma weight residual 120.50 93.58 26.92 3.00e+00 1.11e-01 8.05e+01 angle pdb=" N LYS C 978 " pdb=" CA LYS C 978 " pdb=" C LYS C 978 " ideal model delta sigma weight residual 110.35 121.45 -11.10 1.36e+00 5.41e-01 6.66e+01 angle pdb=" N ARG B 976 " pdb=" CA ARG B 976 " pdb=" C ARG B 976 " ideal model delta sigma weight residual 111.07 119.72 -8.65 1.07e+00 8.73e-01 6.53e+01 ... (remaining 20167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.22: 8649 31.22 - 62.45: 226 62.45 - 93.67: 30 93.67 - 124.90: 3 124.90 - 156.12: 2 Dihedral angle restraints: 8910 sinusoidal: 3598 harmonic: 5312 Sorted by residual: dihedral pdb=" C SER C 979 " pdb=" N SER C 979 " pdb=" CA SER C 979 " pdb=" CB SER C 979 " ideal model delta harmonic sigma weight residual -122.60 -105.03 -17.57 0 2.50e+00 1.60e-01 4.94e+01 dihedral pdb=" CA PRO B 428 " pdb=" C PRO B 428 " pdb=" N PRO B 429 " pdb=" CA PRO B 429 " ideal model delta harmonic sigma weight residual 180.00 144.89 35.11 0 5.00e+00 4.00e-02 4.93e+01 dihedral pdb=" AO3 COA B2002 " pdb=" AP1 COA B2002 " pdb="AO5* COA B2002 " pdb="AC5* COA B2002 " ideal model delta sinusoidal sigma weight residual -68.06 88.06 -156.12 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 8907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.995: 2226 0.995 - 1.990: 0 1.990 - 2.985: 0 2.985 - 3.980: 0 3.980 - 4.975: 1 Chirality restraints: 2227 Sorted by residual: chirality pdb=" CB Y2A B2003 " pdb=" CA Y2A B2003 " pdb=" CG Y2A B2003 " pdb=" OHB Y2A B2003 " both_signs ideal model delta sigma weight residual False 2.51 -2.46 4.97 2.00e-01 2.50e+01 6.19e+02 chirality pdb=" CB THR B 925 " pdb=" CA THR B 925 " pdb=" OG1 THR B 925 " pdb=" CG2 THR B 925 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CB THR A 925 " pdb=" CA THR A 925 " pdb=" OG1 THR A 925 " pdb=" CG2 THR A 925 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.94e+00 ... (remaining 2224 not shown) Planarity restraints: 2573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP B2001 " -0.357 2.00e-02 2.50e+03 3.74e-01 3.15e+03 pdb=" C2' ADP B2001 " 0.461 2.00e-02 2.50e+03 pdb=" C3' ADP B2001 " 0.427 2.00e-02 2.50e+03 pdb=" C4' ADP B2001 " -0.356 2.00e-02 2.50e+03 pdb=" C5' ADP B2001 " 0.393 2.00e-02 2.50e+03 pdb=" N9 ADP B2001 " 0.337 2.00e-02 2.50e+03 pdb=" O2' ADP B2001 " -0.151 2.00e-02 2.50e+03 pdb=" O3' ADP B2001 " -0.241 2.00e-02 2.50e+03 pdb=" O4' ADP B2001 " -0.513 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 428 " 0.060 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO B 429 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 429 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 429 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 979 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C SER D 979 " 0.051 2.00e-02 2.50e+03 pdb=" O SER D 979 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE D 980 " -0.017 2.00e-02 2.50e+03 ... (remaining 2570 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 4 2.24 - 2.91: 5599 2.91 - 3.57: 20263 3.57 - 4.24: 38246 4.24 - 4.90: 63878 Nonbonded interactions: 127990 Sorted by model distance: nonbonded pdb=" AP2 COA B2002 " pdb="AO5* COA B2002 " model vdw 1.576 2.720 nonbonded pdb=" AO6 COA B2002 " pdb=" AP1 COA B2002 " model vdw 1.587 2.720 nonbonded pdb=" O HIS B 975 " pdb=" OD1 ASN B1020 " model vdw 1.686 3.040 nonbonded pdb=" AO6 COA B2002 " pdb="PO10 COA B2002 " model vdw 2.107 2.440 nonbonded pdb=" OH TYR B 199 " pdb=" OE1 GLU B 201 " model vdw 2.267 2.440 ... (remaining 127985 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 821 through 1038 or (resid 1039 and (name N or name CA or \ name C or name O or name CB )) or resid 1040 through 1099)) selection = (chain 'D' and (resid 821 through 1038 or (resid 1039 and (name N or name CA or \ name C or name O or name CB )) or resid 1040 through 1099)) } 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=0.26 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 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: 3.380 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 47.900 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.027 2.261 14915 Z= 1.589 Angle : 1.360 81.766 20172 Z= 0.638 Chirality : 0.123 4.975 2227 Planarity : 0.010 0.374 2573 Dihedral : 14.649 156.123 5530 Min Nonbonded Distance : 1.576 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.71 % Allowed : 0.45 % Favored : 98.84 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 1.15 % Twisted General : 0.17 % 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: -3.80 (0.15), residues: 1859 helix: -3.41 (0.10), residues: 971 sheet: -0.93 (0.43), residues: 141 loop : -1.25 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 877 HIS 0.013 0.002 HIS B 975 PHE 0.028 0.003 PHE B 354 TYR 0.041 0.004 TYR B1093 ARG 0.037 0.002 ARG A 848 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 250 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 243 time to evaluate : 1.782 Fit side-chains REVERT: A 864 LYS cc_start: 0.7997 (mtmt) cc_final: 0.7686 (mptt) REVERT: B 107 ILE cc_start: 0.7545 (mm) cc_final: 0.7109 (mm) REVERT: B 190 ASN cc_start: 0.8146 (m110) cc_final: 0.7791 (m-40) REVERT: C 948 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7754 (ttpt) outliers start: 7 outliers final: 4 residues processed: 247 average time/residue: 1.5586 time to fit residues: 417.4873 Evaluate side-chains 194 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 980 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 HIS A1081 GLN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN B 104 ASN B 645 ASN B 879 GLN ** B 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 GLN C 996 GLN D1081 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14915 Z= 0.180 Angle : 0.725 24.611 20172 Z= 0.326 Chirality : 0.060 1.963 2227 Planarity : 0.005 0.081 2573 Dihedral : 11.168 178.079 2072 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.55 % Allowed : 9.44 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -2.11 (0.17), residues: 1859 helix: -1.61 (0.14), residues: 972 sheet: -0.59 (0.44), residues: 151 loop : -1.00 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 543 HIS 0.004 0.001 HIS D 997 PHE 0.016 0.001 PHE B 405 TYR 0.021 0.001 TYR B 192 ARG 0.006 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 234 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 214 time to evaluate : 1.723 Fit side-chains REVERT: A 864 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7754 (mptt) REVERT: A 965 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7795 (mmtt) REVERT: A 976 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7268 (ptt180) REVERT: B 190 ASN cc_start: 0.8040 (m110) cc_final: 0.7773 (m110) REVERT: B 732 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.6682 (mptt) REVERT: C 948 LYS cc_start: 0.8041 (ttmt) cc_final: 0.7742 (ttpt) REVERT: D 864 LYS cc_start: 0.7744 (mttt) cc_final: 0.7438 (mptt) outliers start: 20 outliers final: 4 residues processed: 223 average time/residue: 1.5004 time to fit residues: 363.4716 Evaluate side-chains 196 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 190 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain B residue 732 LYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 977 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 180 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN B 850 GLN B 888 GLN ** B 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 ASN C 996 GLN D 988 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14915 Z= 0.259 Angle : 0.719 24.949 20172 Z= 0.320 Chirality : 0.060 1.949 2227 Planarity : 0.004 0.078 2573 Dihedral : 10.802 177.453 2069 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.13 % Allowed : 11.96 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.18 (0.18), residues: 1859 helix: -0.63 (0.15), residues: 974 sheet: -0.46 (0.46), residues: 130 loop : -0.85 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 84 HIS 0.004 0.001 HIS D 997 PHE 0.013 0.001 PHE B 959 TYR 0.018 0.002 TYR D 885 ARG 0.004 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 223 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 1.740 Fit side-chains REVERT: A 965 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7777 (mmtt) REVERT: A 976 ARG cc_start: 0.7823 (ptp-110) cc_final: 0.7328 (ptt180) REVERT: B 190 ASN cc_start: 0.8146 (m110) cc_final: 0.7907 (m110) REVERT: B 259 LYS cc_start: 0.8630 (mttm) cc_final: 0.8426 (mttp) REVERT: B 547 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: B 732 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6667 (mptt) REVERT: B 995 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6867 (mmt90) REVERT: C 948 LYS cc_start: 0.8025 (ttmt) cc_final: 0.7704 (ttpt) REVERT: C 1053 ASP cc_start: 0.7202 (m-30) cc_final: 0.6993 (m-30) REVERT: D 864 LYS cc_start: 0.7783 (mttt) cc_final: 0.7375 (mptt) REVERT: D 892 MET cc_start: 0.8594 (mtp) cc_final: 0.8377 (mtp) outliers start: 29 outliers final: 10 residues processed: 211 average time/residue: 1.4349 time to fit residues: 329.8309 Evaluate side-chains 198 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 185 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 732 LYS Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 888 GLN Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain D residue 1015 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 79 optimal weight: 0.2980 chunk 112 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN ** B 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14915 Z= 0.200 Angle : 0.691 24.634 20172 Z= 0.303 Chirality : 0.059 1.951 2227 Planarity : 0.004 0.070 2573 Dihedral : 9.915 167.497 2065 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.07 % Allowed : 13.83 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.59 (0.19), residues: 1859 helix: -0.08 (0.16), residues: 977 sheet: -0.34 (0.46), residues: 149 loop : -0.64 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 40 HIS 0.004 0.001 HIS D 997 PHE 0.011 0.001 PHE B 959 TYR 0.014 0.001 TYR B 192 ARG 0.004 0.000 ARG B 561 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 227 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 1.572 Fit side-chains REVERT: A 976 ARG cc_start: 0.7780 (ptp-110) cc_final: 0.7272 (ptt180) REVERT: B 259 LYS cc_start: 0.8642 (mttm) cc_final: 0.8414 (mttp) REVERT: B 547 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: B 732 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6664 (mptt) REVERT: C 948 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7692 (ttpt) REVERT: C 1053 ASP cc_start: 0.7241 (m-30) cc_final: 0.7020 (m-30) REVERT: D 864 LYS cc_start: 0.7820 (mttt) cc_final: 0.7437 (mptt) outliers start: 27 outliers final: 11 residues processed: 215 average time/residue: 1.5152 time to fit residues: 353.9358 Evaluate side-chains 200 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 187 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 732 LYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain C residue 888 GLN Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain D residue 1015 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 0.4980 chunk 151 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 90 optimal weight: 0.0570 chunk 159 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 ASN D 879 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14915 Z= 0.188 Angle : 0.683 24.261 20172 Z= 0.298 Chirality : 0.059 1.950 2227 Planarity : 0.004 0.063 2573 Dihedral : 9.336 163.159 2065 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.46 % Allowed : 14.29 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.17 (0.19), residues: 1859 helix: 0.30 (0.16), residues: 974 sheet: -0.25 (0.46), residues: 149 loop : -0.46 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 40 HIS 0.003 0.001 HIS D 997 PHE 0.011 0.001 PHE B 959 TYR 0.017 0.001 TYR D 885 ARG 0.005 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 228 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 193 time to evaluate : 1.753 Fit side-chains REVERT: A 881 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8002 (mtp180) REVERT: A 965 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7806 (mmtt) REVERT: A 976 ARG cc_start: 0.7766 (ptp-110) cc_final: 0.7268 (ptt180) REVERT: B 259 LYS cc_start: 0.8644 (mttm) cc_final: 0.8389 (mttp) REVERT: B 547 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: B 732 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6653 (mptt) REVERT: B 1053 ASP cc_start: 0.7726 (t70) cc_final: 0.7464 (t0) REVERT: C 948 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7708 (ttpt) REVERT: C 1053 ASP cc_start: 0.7194 (m-30) cc_final: 0.6955 (m-30) outliers start: 35 outliers final: 14 residues processed: 212 average time/residue: 1.3881 time to fit residues: 321.1935 Evaluate side-chains 200 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 732 LYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1078 ARG Chi-restraints excluded: chain C residue 888 GLN Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain D residue 1015 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.0370 chunk 160 optimal weight: 0.0970 chunk 35 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN ** B 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 ASN C 850 GLN D1024 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14915 Z= 0.174 Angle : 0.677 24.114 20172 Z= 0.294 Chirality : 0.059 1.949 2227 Planarity : 0.003 0.059 2573 Dihedral : 9.106 159.834 2065 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.20 % Allowed : 14.87 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.01 (0.20), residues: 1859 helix: 0.49 (0.16), residues: 977 sheet: -0.20 (0.46), residues: 149 loop : -0.44 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 40 HIS 0.003 0.001 HIS D 997 PHE 0.010 0.001 PHE B 405 TYR 0.015 0.001 TYR B 192 ARG 0.007 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 221 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 1.799 Fit side-chains revert: symmetry clash REVERT: A 844 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8672 (pt) REVERT: A 881 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7844 (mtp180) REVERT: A 976 ARG cc_start: 0.7749 (ptp-110) cc_final: 0.7251 (ptt180) REVERT: B 259 LYS cc_start: 0.8612 (mttm) cc_final: 0.8345 (mttm) REVERT: B 547 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: B 732 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6608 (mptt) REVERT: B 1078 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6954 (mtp-110) REVERT: C 881 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7825 (mtp180) REVERT: C 948 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7720 (ttpt) REVERT: C 995 ARG cc_start: 0.7218 (mmm-85) cc_final: 0.6896 (mmm-85) outliers start: 31 outliers final: 17 residues processed: 208 average time/residue: 1.4851 time to fit residues: 335.8009 Evaluate side-chains 205 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 732 LYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1078 ARG Chi-restraints excluded: chain C residue 881 ARG Chi-restraints excluded: chain C residue 888 GLN Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain D residue 977 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.0050 chunk 20 optimal weight: 0.4980 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS B 539 GLN B 996 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14915 Z= 0.158 Angle : 0.670 23.894 20172 Z= 0.290 Chirality : 0.058 1.947 2227 Planarity : 0.003 0.056 2573 Dihedral : 8.827 157.383 2065 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.26 % Allowed : 15.19 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 1859 helix: 0.70 (0.16), residues: 983 sheet: -0.15 (0.47), residues: 149 loop : -0.39 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 40 HIS 0.005 0.001 HIS C 975 PHE 0.009 0.001 PHE B 959 TYR 0.017 0.001 TYR D 885 ARG 0.006 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 219 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 187 time to evaluate : 1.734 Fit side-chains REVERT: A 844 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8650 (pt) REVERT: A 881 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7991 (mtp180) REVERT: A 976 ARG cc_start: 0.7800 (ptp-110) cc_final: 0.7244 (ptt180) REVERT: B 259 LYS cc_start: 0.8599 (mttm) cc_final: 0.7852 (mtpt) REVERT: B 331 LYS cc_start: 0.8048 (mmmt) cc_final: 0.7840 (mmmt) REVERT: B 547 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: B 732 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6595 (mptt) REVERT: B 957 MET cc_start: 0.7800 (tpp) cc_final: 0.7513 (tpt) REVERT: B 1078 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6866 (mtp-110) REVERT: C 881 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7808 (mtp180) REVERT: C 948 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7739 (ttpt) outliers start: 32 outliers final: 15 residues processed: 206 average time/residue: 1.5352 time to fit residues: 344.1974 Evaluate side-chains 199 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 732 LYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1078 ARG Chi-restraints excluded: chain C residue 881 ARG Chi-restraints excluded: chain C residue 888 GLN Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain D residue 977 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 120 optimal weight: 0.1980 chunk 87 optimal weight: 0.7980 chunk 16 optimal weight: 0.0070 chunk 139 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS B 539 GLN C 961 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14915 Z= 0.170 Angle : 0.679 23.841 20172 Z= 0.293 Chirality : 0.059 1.942 2227 Planarity : 0.003 0.056 2573 Dihedral : 8.487 155.575 2065 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.87 % Allowed : 15.71 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.37 (0.20), residues: 1859 helix: 0.84 (0.16), residues: 984 sheet: -0.11 (0.47), residues: 149 loop : -0.36 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 84 HIS 0.005 0.001 HIS C 975 PHE 0.010 0.001 PHE B 959 TYR 0.018 0.001 TYR B 31 ARG 0.007 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 215 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.611 Fit side-chains REVERT: A 844 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8474 (pt) REVERT: A 881 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7983 (mtp180) REVERT: B 259 LYS cc_start: 0.8599 (mttm) cc_final: 0.7856 (mtpt) REVERT: B 331 LYS cc_start: 0.8074 (mmmt) cc_final: 0.7859 (mmmt) REVERT: B 547 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: B 732 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6611 (mptt) REVERT: B 957 MET cc_start: 0.7820 (tpp) cc_final: 0.7524 (tpt) REVERT: B 1053 ASP cc_start: 0.7704 (t70) cc_final: 0.7473 (t70) REVERT: C 881 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7810 (mtp180) REVERT: C 948 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7766 (ttpt) REVERT: C 995 ARG cc_start: 0.7147 (mmm-85) cc_final: 0.6913 (mmm-85) outliers start: 26 outliers final: 14 residues processed: 204 average time/residue: 1.5617 time to fit residues: 344.8181 Evaluate side-chains 199 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 732 LYS Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain C residue 881 ARG Chi-restraints excluded: chain C residue 888 GLN Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain D residue 977 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 0.0770 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS C 961 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14915 Z= 0.182 Angle : 0.676 23.897 20172 Z= 0.294 Chirality : 0.059 1.938 2227 Planarity : 0.004 0.056 2573 Dihedral : 8.065 147.478 2065 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.94 % Allowed : 16.03 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.41 (0.20), residues: 1859 helix: 0.87 (0.16), residues: 983 sheet: -0.05 (0.47), residues: 145 loop : -0.34 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 84 HIS 0.004 0.001 HIS C 975 PHE 0.010 0.001 PHE B 959 TYR 0.020 0.001 TYR D 885 ARG 0.009 0.000 ARG A1085 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 213 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 1.709 Fit side-chains REVERT: A 881 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7983 (mtp180) REVERT: A 976 ARG cc_start: 0.7844 (ptp-110) cc_final: 0.7474 (ptt180) REVERT: B 259 LYS cc_start: 0.8612 (mttm) cc_final: 0.7881 (mtpt) REVERT: B 331 LYS cc_start: 0.8049 (mmmt) cc_final: 0.7841 (mmmt) REVERT: B 547 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: B 732 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6622 (mptt) REVERT: B 957 MET cc_start: 0.7821 (tpp) cc_final: 0.7506 (tpt) REVERT: B 1053 ASP cc_start: 0.7691 (t70) cc_final: 0.7459 (t0) REVERT: C 881 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7813 (mtp180) REVERT: C 948 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7744 (ttpt) outliers start: 27 outliers final: 16 residues processed: 200 average time/residue: 1.5484 time to fit residues: 335.9168 Evaluate side-chains 200 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 732 LYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain C residue 881 ARG Chi-restraints excluded: chain C residue 888 GLN Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain D residue 977 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 183 optimal weight: 0.3980 chunk 168 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 115 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 879 GLN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS C 961 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14915 Z= 0.160 Angle : 0.677 23.828 20172 Z= 0.293 Chirality : 0.058 1.939 2227 Planarity : 0.004 0.056 2573 Dihedral : 7.829 144.787 2065 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.75 % Allowed : 16.48 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1859 helix: 0.95 (0.16), residues: 983 sheet: 0.00 (0.47), residues: 150 loop : -0.32 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 543 HIS 0.004 0.001 HIS C 975 PHE 0.009 0.001 PHE B 959 TYR 0.018 0.001 TYR B 192 ARG 0.008 0.000 ARG A1085 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 206 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 182 time to evaluate : 1.795 Fit side-chains REVERT: A 844 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8429 (pt) REVERT: A 881 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7962 (mtp180) REVERT: B 259 LYS cc_start: 0.8571 (mttm) cc_final: 0.7844 (mtpt) REVERT: B 732 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6605 (mptt) REVERT: B 957 MET cc_start: 0.7805 (tpp) cc_final: 0.7504 (tpt) REVERT: B 1053 ASP cc_start: 0.7678 (t70) cc_final: 0.7448 (t0) REVERT: C 881 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7789 (mtp180) REVERT: C 948 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7760 (ttpt) outliers start: 24 outliers final: 16 residues processed: 194 average time/residue: 1.5796 time to fit residues: 332.9265 Evaluate side-chains 198 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 178 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 732 LYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain C residue 881 ARG Chi-restraints excluded: chain C residue 888 GLN Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1015 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 879 GLN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 HIS C 900 HIS C 961 ASN D1098 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.150012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127646 restraints weight = 22641.246| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.30 r_work: 0.2992 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 14915 Z= 0.450 Angle : 0.789 24.996 20172 Z= 0.355 Chirality : 0.064 1.915 2227 Planarity : 0.004 0.058 2573 Dihedral : 8.313 141.489 2065 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.33 % Allowed : 16.16 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.05 (0.19), residues: 1859 helix: 0.43 (0.16), residues: 975 sheet: -0.39 (0.47), residues: 140 loop : -0.42 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 84 HIS 0.006 0.001 HIS D 997 PHE 0.016 0.002 PHE B 959 TYR 0.026 0.002 TYR D 885 ARG 0.008 0.001 ARG A1085 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5778.55 seconds wall clock time: 102 minutes 45.19 seconds (6165.19 seconds total)