Starting phenix.real_space_refine on Fri Feb 6 03:12:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x25_66472/02_2026/9x25_66472.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x25_66472/02_2026/9x25_66472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x25_66472/02_2026/9x25_66472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x25_66472/02_2026/9x25_66472.map" model { file = "/net/cci-nas-00/data/ceres_data/9x25_66472/02_2026/9x25_66472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x25_66472/02_2026/9x25_66472.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 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 49 5.49 5 S 31 5.16 5 C 13833 2.51 5 N 3777 2.21 5 O 4120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21810 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 616 Classifications: {'RNA': 29} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna2p': 13, 'rna3p': 15} Chain: "B" Number of atoms: 6800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 6800 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 287} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 933} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1051 Unresolved non-hydrogen angles: 1314 Unresolved non-hydrogen dihedrals: 867 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLU:plan': 48, 'HIS:plan': 8, 'ARG:plan': 20, 'PHE:plan': 9, 'ASN:plan1': 19, 'ASP:plan': 21, 'GLN:plan1': 5, 'TYR:plan': 13} Unresolved non-hydrogen planarities: 617 Chain: "C" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2638 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 16, 'TRANS': 324} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 2, 'ARG:plan': 2, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2348 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 11, 'TRANS': 330} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLU:plan': 21, 'GLN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 9} Unresolved non-hydrogen planarities: 199 Chain: "E" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2363 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 11, 'TRANS': 333} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 372 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 308 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 20, 'GLN:plan1': 3, 'TRP:plan': 2, 'PHE:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 8} Unresolved non-hydrogen planarities: 200 Chain: "F" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2399 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 18, 'GLN:plan1': 3, 'PHE:plan': 1, 'ARG:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 154 Chain: "G" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1110 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 145} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 4, 'ASP:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "H" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1053 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 4, 'TRANS': 144} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 4, 'GLU:plan': 5, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "I" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2054 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 10, 'TRANS': 301} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 593 Unresolved non-hydrogen dihedrals: 396 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ARG:plan': 13, 'GLU:plan': 18, 'TYR:plan': 4, 'PHE:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 14, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 269 Chain: "K" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 429 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Time building chain proxies: 5.08, per 1000 atoms: 0.23 Number of scatterers: 21810 At special positions: 0 Unit cell: (98.56, 133.76, 172.48, 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 31 16.00 P 49 15.00 O 4120 8.00 N 3777 7.00 C 13833 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5520 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 27 sheets defined 50.1% alpha, 12.4% beta 17 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'B' and resid 28 through 38 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 65 through 80 removed outlier: 4.443A pdb=" N SER B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.575A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.576A pdb=" N LYS B 93 " --> pdb=" O SER B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 150 through 179 Processing helix chain 'B' and resid 181 through 203 removed outlier: 6.009A pdb=" N ALA B 194 " --> pdb=" O TRP B 190 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 214 Processing helix chain 'B' and resid 226 through 242 removed outlier: 3.551A pdb=" N HIS B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 257 through 263 Processing helix chain 'B' and resid 266 through 292 removed outlier: 3.769A pdb=" N ALA B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 305 through 315 Processing helix chain 'B' and resid 322 through 328 removed outlier: 4.038A pdb=" N ILE B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 373 removed outlier: 3.580A pdb=" N LEU B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 381 through 388 removed outlier: 3.553A pdb=" N LYS B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 400 removed outlier: 3.679A pdb=" N ILE B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 434 removed outlier: 3.850A pdb=" N LEU B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 Processing helix chain 'B' and resid 462 through 465 Processing helix chain 'B' and resid 466 through 481 Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'B' and resid 535 through 549 Proline residue: B 545 - end of helix removed outlier: 4.714A pdb=" N GLU B 549 " --> pdb=" O PRO B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 removed outlier: 3.987A pdb=" N VAL B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 590 removed outlier: 3.621A pdb=" N VAL B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 626 removed outlier: 3.591A pdb=" N ARG B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 640 removed outlier: 3.500A pdb=" N LEU B 633 " --> pdb=" O PRO B 629 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASN B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ARG B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 646 Processing helix chain 'B' and resid 647 through 651 Processing helix chain 'B' and resid 652 through 661 Processing helix chain 'B' and resid 673 through 694 removed outlier: 3.682A pdb=" N GLU B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 689 " --> pdb=" O ARG B 685 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 692 " --> pdb=" O GLU B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 716 removed outlier: 4.020A pdb=" N LEU B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 735 through 745 Processing helix chain 'B' and resid 750 through 768 Processing helix chain 'B' and resid 768 through 776 Processing helix chain 'B' and resid 797 through 808 Processing helix chain 'B' and resid 835 through 853 Processing helix chain 'B' and resid 877 through 891 removed outlier: 3.646A pdb=" N ASP B 881 " --> pdb=" O GLU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.713A pdb=" N GLU B 901 " --> pdb=" O ARG B 897 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASP B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 925 removed outlier: 4.582A pdb=" N HIS B 915 " --> pdb=" O LYS B 911 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLN B 916 " --> pdb=" O GLU B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 945 removed outlier: 3.630A pdb=" N ALA B 932 " --> pdb=" O ASP B 928 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 964 removed outlier: 3.702A pdb=" N ILE B 957 " --> pdb=" O ASN B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 973 removed outlier: 3.858A pdb=" N THR B 969 " --> pdb=" O ALA B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 998 removed outlier: 3.553A pdb=" N ARG B 986 " --> pdb=" O ARG B 982 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 998 " --> pdb=" O ILE B 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 48 removed outlier: 3.769A pdb=" N LEU C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 128 through 134 Processing helix chain 'C' and resid 217 through 238 removed outlier: 3.930A pdb=" N THR C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 266 removed outlier: 3.974A pdb=" N LEU C 264 " --> pdb=" O ASP C 260 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 332 Processing helix chain 'D' and resid 46 through 64 removed outlier: 3.732A pdb=" N LEU D 50 " --> pdb=" O TRP D 46 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 87 through 97 Processing helix chain 'D' and resid 102 through 110 Processing helix chain 'D' and resid 147 through 166 removed outlier: 3.828A pdb=" N ILE D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 176 Processing helix chain 'D' and resid 213 through 227 Processing helix chain 'D' and resid 235 through 240 Processing helix chain 'D' and resid 247 through 255 Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'E' and resid 46 through 64 removed outlier: 3.762A pdb=" N LEU E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 85 removed outlier: 3.673A pdb=" N GLU E 82 " --> pdb=" O GLU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 97 Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 147 through 166 Processing helix chain 'E' and resid 168 through 175 Processing helix chain 'E' and resid 215 through 227 removed outlier: 3.670A pdb=" N LEU E 226 " --> pdb=" O VAL E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 242 Processing helix chain 'E' and resid 247 through 258 removed outlier: 3.580A pdb=" N PHE E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 324 Processing helix chain 'F' and resid 46 through 64 removed outlier: 3.521A pdb=" N LEU F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 85 removed outlier: 3.811A pdb=" N LYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL F 83 " --> pdb=" O LYS F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 97 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 147 through 165 removed outlier: 3.680A pdb=" N LEU F 160 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 175 removed outlier: 3.753A pdb=" N ILE F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.856A pdb=" N GLU F 217 " --> pdb=" O SER F 213 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN F 218 " --> pdb=" O ASN F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 242 removed outlier: 3.738A pdb=" N ILE F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 258 Processing helix chain 'F' and resid 311 through 323 Processing helix chain 'G' and resid 5 through 25 removed outlier: 3.569A pdb=" N GLU G 9 " --> pdb=" O GLU G 5 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 49 Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 50 through 62 Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 75 through 79 Processing helix chain 'G' and resid 81 through 101 Processing helix chain 'G' and resid 116 through 123 Processing helix chain 'G' and resid 125 through 151 Processing helix chain 'H' and resid 5 through 24 Processing helix chain 'H' and resid 28 through 62 removed outlier: 3.537A pdb=" N GLN H 32 " --> pdb=" O ASN H 28 " (cutoff:3.500A) Proline residue: H 43 - end of helix removed outlier: 3.516A pdb=" N ILE H 46 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU H 51 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N GLY H 52 " --> pdb=" O ASN H 48 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA H 53 " --> pdb=" O ASN H 49 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU H 62 " --> pdb=" O PHE H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 79 Processing helix chain 'H' and resid 81 through 101 Processing helix chain 'H' and resid 116 through 123 Processing helix chain 'H' and resid 125 through 151 removed outlier: 3.668A pdb=" N VAL H 129 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS H 145 " --> pdb=" O ASN H 141 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET H 150 " --> pdb=" O PHE H 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 24 removed outlier: 3.693A pdb=" N LYS I 24 " --> pdb=" O GLU I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 38 Processing helix chain 'I' and resid 53 through 61 Processing helix chain 'I' and resid 63 through 77 Processing helix chain 'I' and resid 78 through 96 Processing helix chain 'I' and resid 135 through 155 removed outlier: 3.542A pdb=" N LEU I 139 " --> pdb=" O PRO I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 163 Processing helix chain 'I' and resid 163 through 179 Processing helix chain 'I' and resid 188 through 201 Processing helix chain 'I' and resid 205 through 211 removed outlier: 3.733A pdb=" N GLY I 208 " --> pdb=" O ASP I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 232 Processing helix chain 'I' and resid 248 through 255 removed outlier: 3.588A pdb=" N LEU I 252 " --> pdb=" O THR I 248 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP I 254 " --> pdb=" O GLU I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 324 Processing helix chain 'I' and resid 329 through 333 removed outlier: 3.674A pdb=" N GLY I 333 " --> pdb=" O THR I 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 95 through 97 Processing sheet with id=AA2, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AA3, first strand: chain 'B' and resid 297 through 299 removed outlier: 5.975A pdb=" N VAL B 297 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU B 338 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR B 299 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 779 through 784 removed outlier: 6.962A pdb=" N LEU B 789 " --> pdb=" O ILE B 781 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER B 783 " --> pdb=" O ASP B 787 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP B 787 " --> pdb=" O SER B 783 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N ALA B 859 " --> pdb=" O LEU B 823 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA B 825 " --> pdb=" O ALA B 859 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLY B 861 " --> pdb=" O ALA B 825 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 827 " --> pdb=" O GLY B 861 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU B 863 " --> pdb=" O LEU B 827 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE B 829 " --> pdb=" O LEU B 863 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 812 through 813 Processing sheet with id=AA6, first strand: chain 'C' and resid 142 through 143 removed outlier: 6.881A pdb=" N GLU C 84 " --> pdb=" O HIS C 70 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N HIS C 70 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C 69 " --> pdb=" O TRP C 187 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N CYS C 182 " --> pdb=" O PRO C 7 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 6 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 200 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 149 through 159 removed outlier: 5.577A pdb=" N HIS C 169 " --> pdb=" O ALA C 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 278 removed outlier: 6.720A pdb=" N GLU C 311 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL C 275 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE C 309 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE C 277 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL C 307 " --> pdb=" O PHE C 277 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 283 through 285 Processing sheet with id=AB1, first strand: chain 'C' and resid 288 through 289 Processing sheet with id=AB2, first strand: chain 'D' and resid 7 through 9 Processing sheet with id=AB3, first strand: chain 'D' and resid 44 through 45 removed outlier: 6.532A pdb=" N PHE D 144 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 44 through 45 removed outlier: 6.767A pdb=" N LEU D 290 " --> pdb=" O LEU D 131 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 326 " --> pdb=" O VAL D 343 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 201 through 202 Processing sheet with id=AB6, first strand: chain 'D' and resid 260 through 264 Processing sheet with id=AB7, first strand: chain 'E' and resid 44 through 45 removed outlier: 5.713A pdb=" N PHE E 144 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 44 through 45 removed outlier: 7.299A pdb=" N ALA E 128 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N LEU E 294 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE E 130 " --> pdb=" O TYR E 292 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR E 292 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA E 326 " --> pdb=" O VAL E 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 185 through 186 removed outlier: 3.537A pdb=" N VAL E 200 " --> pdb=" O LEU E 207 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 230 through 231 Processing sheet with id=AC2, first strand: chain 'E' and resid 260 through 262 Processing sheet with id=AC3, first strand: chain 'F' and resid 44 through 45 Processing sheet with id=AC4, first strand: chain 'F' and resid 44 through 45 Processing sheet with id=AC5, first strand: chain 'F' and resid 133 through 135 removed outlier: 6.095A pdb=" N PHE F 144 " --> pdb=" O ALA F 244 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL F 246 " --> pdb=" O PHE F 144 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR F 146 " --> pdb=" O VAL F 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 260 through 267 removed outlier: 5.788A pdb=" N GLY F 278 " --> pdb=" O ARG F 266 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 240 through 242 removed outlier: 4.067A pdb=" N ARG I 104 " --> pdb=" O ASP I 338 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 214 through 217 Processing sheet with id=AC9, first strand: chain 'I' and resid 259 through 261 1170 hydrogen bonds defined for protein. 3324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 4.27 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6342 1.33 - 1.45: 3642 1.45 - 1.57: 12179 1.57 - 1.69: 97 1.69 - 1.81: 55 Bond restraints: 22315 Sorted by residual: bond pdb=" CG1 ILE G 139 " pdb=" CD1 ILE G 139 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.61e+00 bond pdb=" C PHE E 144 " pdb=" N VAL E 145 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.29e-02 6.01e+03 1.15e+00 bond pdb=" CA ASP B 928 " pdb=" C ASP B 928 " ideal model delta sigma weight residual 1.532 1.521 0.011 1.12e-02 7.97e+03 1.00e+00 bond pdb=" C GLY F 140 " pdb=" N VAL F 141 " ideal model delta sigma weight residual 1.327 1.300 0.028 2.97e-02 1.13e+03 8.71e-01 bond pdb=" CG MET E 291 " pdb=" SD MET E 291 " ideal model delta sigma weight residual 1.803 1.780 0.023 2.50e-02 1.60e+03 8.37e-01 ... (remaining 22310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 30214 1.77 - 3.54: 340 3.54 - 5.31: 42 5.31 - 7.08: 10 7.08 - 8.85: 3 Bond angle restraints: 30609 Sorted by residual: angle pdb=" C ASP B 928 " pdb=" CA ASP B 928 " pdb=" CB ASP B 928 " ideal model delta sigma weight residual 116.34 110.54 5.80 1.40e+00 5.10e-01 1.72e+01 angle pdb=" O4' G A 21 " pdb=" C1' G A 21 " pdb=" N9 G A 21 " ideal model delta sigma weight residual 108.20 113.79 -5.59 1.50e+00 4.44e-01 1.39e+01 angle pdb=" O4' G A 27 " pdb=" C1' G A 27 " pdb=" N9 G A 27 " ideal model delta sigma weight residual 108.50 113.72 -5.22 1.50e+00 4.44e-01 1.21e+01 angle pdb=" O3' G A 4 " pdb=" C3' G A 4 " pdb=" C2' G A 4 " ideal model delta sigma weight residual 113.70 118.56 -4.86 1.50e+00 4.44e-01 1.05e+01 angle pdb=" CA GLU H 134 " pdb=" CB GLU H 134 " pdb=" CG GLU H 134 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.14e+00 ... (remaining 30604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.53: 12187 26.53 - 53.05: 874 53.05 - 79.58: 132 79.58 - 106.10: 7 106.10 - 132.62: 2 Dihedral angle restraints: 13202 sinusoidal: 4681 harmonic: 8521 Sorted by residual: dihedral pdb=" CA ASN I 12 " pdb=" C ASN I 12 " pdb=" N SER I 13 " pdb=" CA SER I 13 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA VAL E 141 " pdb=" C VAL E 141 " pdb=" N PHE E 142 " pdb=" CA PHE E 142 " ideal model delta harmonic sigma weight residual 180.00 159.02 20.98 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" O4' G A 20 " pdb=" C1' G A 20 " pdb=" N9 G A 20 " pdb=" C4 G A 20 " ideal model delta sinusoidal sigma weight residual -106.00 -166.73 60.73 1 1.70e+01 3.46e-03 1.70e+01 ... (remaining 13199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3255 0.062 - 0.124: 384 0.124 - 0.186: 10 0.186 - 0.247: 5 0.247 - 0.309: 1 Chirality restraints: 3655 Sorted by residual: chirality pdb=" C1' G A 21 " pdb=" O4' G A 21 " pdb=" C2' G A 21 " pdb=" N9 G A 21 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3' G A 4 " pdb=" C4' G A 4 " pdb=" O3' G A 4 " pdb=" C2' G A 4 " both_signs ideal model delta sigma weight residual False -2.48 -2.25 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C4' G A 27 " pdb=" C5' G A 27 " pdb=" O4' G A 27 " pdb=" C3' G A 27 " both_signs ideal model delta sigma weight residual False -2.50 -2.28 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3652 not shown) Planarity restraints: 3768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A 25 " -0.040 2.00e-02 2.50e+03 2.14e-02 1.03e+01 pdb=" N1 U A 25 " 0.047 2.00e-02 2.50e+03 pdb=" C2 U A 25 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U A 25 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U A 25 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U A 25 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U A 25 " -0.013 2.00e-02 2.50e+03 pdb=" C5 U A 25 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U A 25 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 13 " 0.036 2.00e-02 2.50e+03 1.68e-02 7.74e+00 pdb=" N9 A A 13 " -0.039 2.00e-02 2.50e+03 pdb=" C8 A A 13 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A A 13 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A 13 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A A 13 " -0.000 2.00e-02 2.50e+03 pdb=" N6 A A 13 " 0.012 2.00e-02 2.50e+03 pdb=" N1 A A 13 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A A 13 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A A 13 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A A 13 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 27 " 0.035 2.00e-02 2.50e+03 1.60e-02 7.72e+00 pdb=" N9 G A 27 " -0.041 2.00e-02 2.50e+03 pdb=" C8 G A 27 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G A 27 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G A 27 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A 27 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G A 27 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G A 27 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 27 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G A 27 " -0.008 2.00e-02 2.50e+03 pdb=" N3 G A 27 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G A 27 " -0.002 2.00e-02 2.50e+03 ... (remaining 3765 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 12202 2.99 - 3.47: 23430 3.47 - 3.95: 34473 3.95 - 4.42: 40301 4.42 - 4.90: 63177 Nonbonded interactions: 173583 Sorted by model distance: nonbonded pdb=" O5' DC K 11 " pdb=" O4' DC K 11 " model vdw 2.513 2.432 nonbonded pdb=" O6 G A 18 " pdb=" N6 DA K 23 " model vdw 2.514 3.120 nonbonded pdb=" C THR B 750 " pdb=" OG1 THR B 750 " model vdw 2.528 2.616 nonbonded pdb=" O5' DA K 14 " pdb=" O4' DA K 14 " model vdw 2.566 2.432 nonbonded pdb=" N1 G A 27 " pdb=" C4 G A 27 " model vdw 2.576 2.672 ... (remaining 173578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 24 or resid 30 through 62 or (resid 63 through 103 and (nam \ e N or name CA or name C or name O or name CB )) or resid 104 through 110 or (re \ sid 111 through 114 and (name N or name CA or name C or name O or name CB )) or \ (resid 115 through 120 and (name N or name CA or name C or name O or name CB )) \ or resid 121 through 158 or (resid 159 and (name N or name CA or name C or name \ O or name CB )) or resid 160 or (resid 161 through 185 and (name N or name CA or \ name C or name O or name CB )) or resid 186 through 266 or (resid 267 through 2 \ 71 and (name N or name CA or name C or name O or name CB )) or resid 272 or (res \ id 273 through 276 and (name N or name CA or name C or name O or name CB )) or r \ esid 277 through 300 or (resid 301 through 314 and (name N or name CA or name C \ or name O or name CB )) or resid 315 through 345)) selection = (chain 'E' and (resid 4 through 24 or resid 30 through 99 or (resid 100 through \ 103 and (name N or name CA or name C or name O or name CB )) or resid 104 throug \ h 110 or (resid 111 through 114 and (name N or name CA or name C or name O or na \ me CB )) or (resid 115 through 120 and (name N or name CA or name C or name O or \ name CB )) or resid 121 through 158 or (resid 159 and (name N or name CA or nam \ e C or name O or name CB )) or resid 160 or (resid 161 through 185 and (name N o \ r name CA or name C or name O or name CB )) or resid 186 through 213 or (resid 2 \ 14 through 227 and (name N or name CA or name C or name O or name CB )) or resid \ 228 through 345)) selection = (chain 'F' and (resid 4 through 62 or (resid 63 through 103 and (name N or name \ CA or name C or name O or name CB )) or resid 104 through 173 or (resid 174 thro \ ugh 185 and (name N or name CA or name C or name O or name CB )) or resid 186 th \ rough 213 or (resid 214 through 227 and (name N or name CA or name C or name O o \ r name CB )) or resid 228 or (resid 229 through 232 and (name N or name CA or na \ me C or name O or name CB )) or resid 233 or (resid 234 through 241 and (name N \ or name CA or name C or name O or name CB )) or resid 242 through 266 or (resid \ 267 through 271 and (name N or name CA or name C or name O or name CB )) or resi \ d 272 or (resid 273 through 276 and (name N or name CA or name C or name O or na \ me CB )) or resid 277 through 345)) } ncs_group { reference = (chain 'G' and (resid 4 through 19 or (resid 20 through 30 and (name N or name C \ A or name C or name O or name CB )) or resid 31 through 40 or (resid 41 through \ 42 and (name N or name CA or name C or name O or name CB )) or resid 43 through \ 62 or (resid 63 through 68 and (name N or name CA or name C or name O or name CB \ )) or resid 69 through 72 or (resid 73 through 79 and (name N or name CA or nam \ e C or name O or name CB )) or resid 80 through 107 or (resid 108 through 109 an \ d (name N or name CA or name C or name O or name CB )) or resid 110 or (resid 11 \ 1 through 113 and (name N or name CA or name C or name O or name CB )) or resid \ 114 through 151)) selection = (chain 'H' and (resid 4 through 39 or (resid 40 through 42 and (name N or name C \ A or name C or name O or name CB )) or resid 43 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 75 or (resi \ d 76 through 79 and (name N or name CA or name C or name O or name CB )) or (res \ id 80 through 86 and (name N or name CA or name C or name O or name CB )) or res \ id 87 through 115 or (resid 116 and (name N or name CA or name C or name O or na \ me CB )) or resid 117 through 151)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.950 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22315 Z= 0.193 Angle : 0.508 8.851 30609 Z= 0.277 Chirality : 0.040 0.309 3655 Planarity : 0.003 0.038 3768 Dihedral : 17.649 132.625 7682 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.29 % Allowed : 28.06 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.16), residues: 2920 helix: 2.14 (0.14), residues: 1339 sheet: -0.60 (0.27), residues: 365 loop : -0.84 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 271 TYR 0.010 0.001 TYR F 14 PHE 0.028 0.001 PHE F 142 TRP 0.013 0.001 TRP B 517 HIS 0.007 0.001 HIS F 20 Details of bonding type rmsd covalent geometry : bond 0.00420 (22315) covalent geometry : angle 0.50829 (30609) hydrogen bonds : bond 0.14665 ( 1205) hydrogen bonds : angle 6.41645 ( 3410) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 46 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 157 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8726 (m-80) REVERT: B 163 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8851 (ptt180) REVERT: B 917 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8848 (tt) REVERT: C 75 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.8666 (t80) REVERT: D 158 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8983 (m-10) REVERT: E 152 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8346 (tp40) REVERT: E 291 MET cc_start: 0.8587 (mmm) cc_final: 0.7946 (mmm) REVERT: G 5 GLU cc_start: 0.8285 (mp0) cc_final: 0.7995 (mp0) REVERT: H 150 MET cc_start: 0.8933 (ptm) cc_final: 0.8395 (ppp) REVERT: I 198 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8587 (tm-30) outliers start: 76 outliers final: 68 residues processed: 121 average time/residue: 0.1363 time to fit residues: 28.8850 Evaluate side-chains 120 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 46 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 443 LYS Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 799 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 943 HIS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain H residue 87 TYR Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 298 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.0980 chunk 111 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.044861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.037586 restraints weight = 178129.428| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 4.34 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22315 Z= 0.099 Angle : 0.445 7.805 30609 Z= 0.244 Chirality : 0.039 0.262 3655 Planarity : 0.003 0.036 3768 Dihedral : 13.432 134.768 3913 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.56 % Allowed : 27.84 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.16), residues: 2920 helix: 2.45 (0.14), residues: 1356 sheet: -0.57 (0.27), residues: 372 loop : -0.73 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 523 TYR 0.008 0.001 TYR F 292 PHE 0.026 0.001 PHE F 142 TRP 0.013 0.001 TRP B 517 HIS 0.005 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00192 (22315) covalent geometry : angle 0.44488 (30609) hydrogen bonds : bond 0.03723 ( 1205) hydrogen bonds : angle 4.58681 ( 3410) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 45 time to evaluate : 0.869 Fit side-chains REVERT: B 157 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8774 (m-80) REVERT: B 163 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8854 (ptt180) REVERT: B 450 MET cc_start: 0.8997 (tmm) cc_final: 0.8604 (tmm) REVERT: C 75 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8434 (t80) REVERT: D 158 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8862 (m-10) REVERT: G 5 GLU cc_start: 0.8494 (mp0) cc_final: 0.8038 (pm20) REVERT: H 150 MET cc_start: 0.8772 (ptm) cc_final: 0.8327 (ppp) REVERT: I 198 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8649 (tm-30) outliers start: 63 outliers final: 26 residues processed: 107 average time/residue: 0.1338 time to fit residues: 24.9168 Evaluate side-chains 73 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 43 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 943 HIS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 326 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 177 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 230 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 248 optimal weight: 0.0050 chunk 120 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 255 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 106 optimal weight: 0.2980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.045310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.038053 restraints weight = 178341.905| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 4.36 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22315 Z= 0.087 Angle : 0.427 7.540 30609 Z= 0.231 Chirality : 0.039 0.250 3655 Planarity : 0.003 0.035 3768 Dihedral : 12.994 135.345 3827 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.56 % Allowed : 27.33 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.16), residues: 2920 helix: 2.55 (0.14), residues: 1358 sheet: -0.40 (0.27), residues: 368 loop : -0.68 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 207 TYR 0.008 0.001 TYR H 87 PHE 0.024 0.001 PHE F 142 TRP 0.012 0.001 TRP B 517 HIS 0.004 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00178 (22315) covalent geometry : angle 0.42700 (30609) hydrogen bonds : bond 0.03138 ( 1205) hydrogen bonds : angle 4.15983 ( 3410) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 48 time to evaluate : 0.875 Fit side-chains REVERT: B 157 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8825 (m-80) REVERT: B 450 MET cc_start: 0.8911 (tmm) cc_final: 0.8549 (tmm) REVERT: C 75 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8413 (t80) REVERT: D 158 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8824 (m-10) REVERT: E 51 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8562 (tttt) REVERT: G 5 GLU cc_start: 0.8503 (mp0) cc_final: 0.8235 (mp0) REVERT: G 150 MET cc_start: 0.7661 (tmm) cc_final: 0.7407 (tmm) REVERT: H 150 MET cc_start: 0.8663 (ptm) cc_final: 0.8373 (ppp) outliers start: 63 outliers final: 34 residues processed: 109 average time/residue: 0.1453 time to fit residues: 26.4690 Evaluate side-chains 83 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 45 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 943 HIS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 219 CYS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 89 TYR Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 326 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 23 optimal weight: 6.9990 chunk 292 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 177 optimal weight: 20.0000 chunk 224 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 234 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.044716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.037454 restraints weight = 178271.824| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 4.32 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22315 Z= 0.135 Angle : 0.447 7.471 30609 Z= 0.242 Chirality : 0.039 0.272 3655 Planarity : 0.003 0.034 3768 Dihedral : 12.962 133.981 3820 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.33 % Allowed : 27.84 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.16), residues: 2920 helix: 2.60 (0.14), residues: 1358 sheet: -0.43 (0.27), residues: 368 loop : -0.71 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 256 TYR 0.009 0.001 TYR B 444 PHE 0.026 0.001 PHE F 142 TRP 0.011 0.001 TRP B 517 HIS 0.005 0.001 HIS F 20 Details of bonding type rmsd covalent geometry : bond 0.00297 (22315) covalent geometry : angle 0.44660 (30609) hydrogen bonds : bond 0.03228 ( 1205) hydrogen bonds : angle 4.11995 ( 3410) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 45 time to evaluate : 1.032 Fit side-chains REVERT: B 157 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.8773 (m-80) REVERT: B 913 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7590 (m-10) REVERT: D 158 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8866 (m-10) REVERT: E 291 MET cc_start: 0.8328 (mmm) cc_final: 0.8069 (mmm) REVERT: G 5 GLU cc_start: 0.8481 (mp0) cc_final: 0.8179 (mp0) outliers start: 59 outliers final: 41 residues processed: 104 average time/residue: 0.1296 time to fit residues: 23.8738 Evaluate side-chains 86 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 42 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 768 HIS Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 913 PHE Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 943 HIS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 219 CYS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain H residue 87 TYR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 89 TYR Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 326 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 200 optimal weight: 5.9990 chunk 114 optimal weight: 0.0050 chunk 294 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 478 ASN B 925 HIS ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.043464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.036179 restraints weight = 181437.126| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.29 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22315 Z= 0.236 Angle : 0.536 10.333 30609 Z= 0.289 Chirality : 0.041 0.332 3655 Planarity : 0.003 0.043 3768 Dihedral : 13.037 131.161 3816 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.69 % Allowed : 27.56 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.16), residues: 2920 helix: 2.43 (0.14), residues: 1348 sheet: -0.58 (0.26), residues: 376 loop : -0.84 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 271 TYR 0.013 0.001 TYR H 87 PHE 0.028 0.001 PHE F 142 TRP 0.013 0.001 TRP B 517 HIS 0.008 0.001 HIS F 20 Details of bonding type rmsd covalent geometry : bond 0.00520 (22315) covalent geometry : angle 0.53642 (30609) hydrogen bonds : bond 0.03874 ( 1205) hydrogen bonds : angle 4.39268 ( 3410) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 43 time to evaluate : 0.736 Fit side-chains REVERT: B 157 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8748 (m-80) REVERT: B 440 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8348 (tp) REVERT: B 746 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8161 (ptm160) REVERT: B 913 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7648 (m-10) REVERT: C 214 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8332 (mtm-85) REVERT: D 158 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8930 (m-10) REVERT: I 7 VAL cc_start: 0.9265 (OUTLIER) cc_final: 0.9059 (t) outliers start: 83 outliers final: 57 residues processed: 126 average time/residue: 0.1130 time to fit residues: 24.1415 Evaluate side-chains 105 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 41 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 746 ARG Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 799 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 913 PHE Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 943 HIS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 219 CYS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain H residue 87 TYR Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 326 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 137 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 925 HIS E 48 GLN I 145 HIS ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.044398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.037140 restraints weight = 179779.669| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 4.32 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22315 Z= 0.118 Angle : 0.462 10.485 30609 Z= 0.248 Chirality : 0.040 0.282 3655 Planarity : 0.003 0.036 3768 Dihedral : 12.984 133.136 3816 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.95 % Allowed : 28.74 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.16), residues: 2920 helix: 2.54 (0.14), residues: 1360 sheet: -0.48 (0.26), residues: 371 loop : -0.77 (0.19), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 256 TYR 0.010 0.001 TYR H 87 PHE 0.025 0.001 PHE F 142 TRP 0.011 0.001 TRP B 517 HIS 0.005 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00255 (22315) covalent geometry : angle 0.46152 (30609) hydrogen bonds : bond 0.03322 ( 1205) hydrogen bonds : angle 4.12467 ( 3410) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 43 time to evaluate : 0.840 Fit side-chains REVERT: B 157 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: B 714 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9035 (mm) REVERT: B 746 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8086 (ptm160) REVERT: B 913 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7535 (m-10) REVERT: C 75 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8362 (t80) REVERT: D 158 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8810 (m-10) REVERT: G 5 GLU cc_start: 0.8572 (mp0) cc_final: 0.8156 (pm20) REVERT: H 150 MET cc_start: 0.8738 (ptm) cc_final: 0.8235 (ppp) outliers start: 70 outliers final: 47 residues processed: 113 average time/residue: 0.1260 time to fit residues: 24.7586 Evaluate side-chains 95 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 42 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 746 ARG Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 768 HIS Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 913 PHE Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 943 HIS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 219 CYS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain H residue 87 TYR Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 89 TYR Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 326 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 13 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 275 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 116 optimal weight: 0.0070 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 925 HIS ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.043680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.036394 restraints weight = 180400.397| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 4.29 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22315 Z= 0.200 Angle : 0.515 8.947 30609 Z= 0.277 Chirality : 0.041 0.313 3655 Planarity : 0.003 0.040 3768 Dihedral : 13.012 132.015 3816 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.35 % Allowed : 28.29 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.16), residues: 2920 helix: 2.48 (0.14), residues: 1348 sheet: -0.59 (0.26), residues: 385 loop : -0.84 (0.19), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 271 TYR 0.012 0.001 TYR H 87 PHE 0.026 0.001 PHE F 142 TRP 0.014 0.001 TRP C 227 HIS 0.013 0.001 HIS I 145 Details of bonding type rmsd covalent geometry : bond 0.00442 (22315) covalent geometry : angle 0.51464 (30609) hydrogen bonds : bond 0.03658 ( 1205) hydrogen bonds : angle 4.25458 ( 3410) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 43 time to evaluate : 0.598 Fit side-chains REVERT: B 157 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8712 (m-80) REVERT: B 440 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8434 (tp) REVERT: B 714 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9094 (mm) REVERT: B 746 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8162 (ptm160) REVERT: B 913 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7628 (m-10) REVERT: D 158 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8859 (m-10) REVERT: G 5 GLU cc_start: 0.8596 (mp0) cc_final: 0.8218 (pm20) outliers start: 77 outliers final: 57 residues processed: 120 average time/residue: 0.1200 time to fit residues: 25.1258 Evaluate side-chains 105 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 42 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 746 ARG Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 768 HIS Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 913 PHE Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 943 HIS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 219 CYS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain H residue 87 TYR Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 326 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 85 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 238 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.044761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.037500 restraints weight = 177996.282| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.32 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22315 Z= 0.101 Angle : 0.456 8.017 30609 Z= 0.244 Chirality : 0.039 0.269 3655 Planarity : 0.003 0.037 3768 Dihedral : 12.954 134.104 3816 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.27 % Allowed : 29.19 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.16), residues: 2920 helix: 2.56 (0.14), residues: 1361 sheet: -0.50 (0.26), residues: 366 loop : -0.75 (0.19), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 256 TYR 0.010 0.001 TYR F 292 PHE 0.025 0.001 PHE F 142 TRP 0.010 0.001 TRP G 97 HIS 0.006 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00215 (22315) covalent geometry : angle 0.45595 (30609) hydrogen bonds : bond 0.03138 ( 1205) hydrogen bonds : angle 4.00910 ( 3410) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 46 time to evaluate : 1.009 Fit side-chains REVERT: B 157 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8728 (m-80) REVERT: B 714 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.9009 (mm) REVERT: B 913 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7650 (m-10) REVERT: D 158 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8746 (m-10) REVERT: E 51 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8531 (tttt) REVERT: G 5 GLU cc_start: 0.8637 (mp0) cc_final: 0.8271 (pm20) REVERT: H 150 MET cc_start: 0.8673 (ptm) cc_final: 0.8246 (ppp) outliers start: 58 outliers final: 47 residues processed: 104 average time/residue: 0.1237 time to fit residues: 22.7339 Evaluate side-chains 97 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 45 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 768 HIS Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 913 PHE Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 943 HIS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 219 CYS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain H residue 87 TYR Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 326 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 110 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 271 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 chunk 188 optimal weight: 0.0770 chunk 125 optimal weight: 4.9990 chunk 221 optimal weight: 0.7980 chunk 269 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.044341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.037073 restraints weight = 179298.219| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 4.31 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22315 Z= 0.138 Angle : 0.476 8.323 30609 Z= 0.254 Chirality : 0.040 0.282 3655 Planarity : 0.003 0.036 3768 Dihedral : 12.937 133.294 3816 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.99 % Allowed : 29.64 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.16), residues: 2920 helix: 2.58 (0.14), residues: 1359 sheet: -0.62 (0.26), residues: 383 loop : -0.72 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 256 TYR 0.008 0.001 TYR F 292 PHE 0.025 0.001 PHE F 142 TRP 0.013 0.001 TRP C 227 HIS 0.005 0.001 HIS F 20 Details of bonding type rmsd covalent geometry : bond 0.00304 (22315) covalent geometry : angle 0.47615 (30609) hydrogen bonds : bond 0.03247 ( 1205) hydrogen bonds : angle 4.04169 ( 3410) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 44 time to evaluate : 0.738 Fit side-chains REVERT: B 157 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8697 (m-80) REVERT: B 440 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8465 (tp) REVERT: B 714 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9031 (mm) REVERT: B 913 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7629 (m-10) REVERT: C 75 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8390 (t80) REVERT: D 158 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8796 (m-10) REVERT: G 5 GLU cc_start: 0.8604 (mp0) cc_final: 0.8246 (pm20) REVERT: H 150 MET cc_start: 0.8705 (ptm) cc_final: 0.8228 (ppp) outliers start: 53 outliers final: 46 residues processed: 97 average time/residue: 0.1165 time to fit residues: 20.3610 Evaluate side-chains 95 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 43 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 768 HIS Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 913 PHE Chi-restraints excluded: chain B residue 920 TYR Chi-restraints excluded: chain B residue 943 HIS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 219 CYS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain H residue 87 TYR Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 288 PHE Chi-restraints excluded: chain I residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 191 optimal weight: 0.0470 chunk 73 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 277 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 chunk 158 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 47 optimal weight: 0.0570 chunk 1 optimal weight: 9.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.045109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.037838 restraints weight = 177863.598| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 4.34 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22315 Z= 0.091 Angle : 0.454 8.663 30609 Z= 0.240 Chirality : 0.039 0.256 3655 Planarity : 0.003 0.037 3768 Dihedral : 12.891 135.063 3816 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.22 % Allowed : 29.42 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.16), residues: 2920 helix: 2.64 (0.14), residues: 1359 sheet: -0.45 (0.27), residues: 366 loop : -0.65 (0.19), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 256 TYR 0.009 0.001 TYR F 292 PHE 0.025 0.001 PHE F 142 TRP 0.010 0.001 TRP G 97 HIS 0.006 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00195 (22315) covalent geometry : angle 0.45381 (30609) hydrogen bonds : bond 0.02933 ( 1205) hydrogen bonds : angle 3.90814 ( 3410) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 47 time to evaluate : 0.913 Fit side-chains REVERT: B 157 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8739 (m-80) REVERT: B 714 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8956 (mm) REVERT: B 913 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7664 (m-10) REVERT: C 75 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8352 (t80) REVERT: D 158 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8703 (m-10) REVERT: D 294 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8346 (mp) REVERT: G 5 GLU cc_start: 0.8652 (mp0) cc_final: 0.8291 (pm20) REVERT: H 150 MET cc_start: 0.8621 (ptm) cc_final: 0.8279 (ppp) outliers start: 57 outliers final: 46 residues processed: 104 average time/residue: 0.1327 time to fit residues: 24.2801 Evaluate side-chains 98 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 46 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 768 HIS Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 913 PHE Chi-restraints excluded: chain B residue 943 HIS Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 219 CYS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain H residue 87 TYR Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 281 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 254 optimal weight: 0.0270 chunk 215 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.044467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.037166 restraints weight = 179916.549| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 4.34 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22315 Z= 0.139 Angle : 0.476 8.735 30609 Z= 0.254 Chirality : 0.040 0.278 3655 Planarity : 0.003 0.036 3768 Dihedral : 12.872 133.426 3814 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.27 % Allowed : 29.42 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.16), residues: 2920 helix: 2.65 (0.14), residues: 1352 sheet: -0.53 (0.26), residues: 374 loop : -0.62 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 271 TYR 0.008 0.001 TYR F 292 PHE 0.025 0.001 PHE F 142 TRP 0.011 0.001 TRP B 517 HIS 0.005 0.001 HIS F 20 Details of bonding type rmsd covalent geometry : bond 0.00308 (22315) covalent geometry : angle 0.47618 (30609) hydrogen bonds : bond 0.03194 ( 1205) hydrogen bonds : angle 3.98221 ( 3410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3167.02 seconds wall clock time: 55 minutes 42.69 seconds (3342.69 seconds total)