Starting phenix.real_space_refine on Thu Mar 5 08:13:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7apx_11859/03_2026/7apx_11859.cif Found real_map, /net/cci-nas-00/data/ceres_data/7apx_11859/03_2026/7apx_11859.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/7apx_11859/03_2026/7apx_11859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7apx_11859/03_2026/7apx_11859.map" model { file = "/net/cci-nas-00/data/ceres_data/7apx_11859/03_2026/7apx_11859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7apx_11859/03_2026/7apx_11859.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= 0.002 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 13246 2.51 5 N 3517 2.21 5 O 3721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20552 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 8127 Classifications: {'peptide': 1146} Incomplete info: {'truncation_to_alanine': 356} Link IDs: {'PTRANS': 33, 'TRANS': 1112} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1217 Unresolved non-hydrogen angles: 1518 Unresolved non-hydrogen dihedrals: 969 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 16, 'GLU:plan': 63, 'ARG:plan': 19, 'ASN:plan1': 30, 'TRP:plan': 2, 'ASP:plan': 36, 'PHE:plan': 7, 'HIS:plan': 5, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 722 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4143 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 22, 'TRANS': 540} Chain breaks: 3 Unresolved non-hydrogen bonds: 560 Unresolved non-hydrogen angles: 680 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASN:plan1': 15, 'GLU:plan': 35, 'GLN:plan1': 5, 'HIS:plan': 1, 'ASP:plan': 24, 'ARG:plan': 10, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 358 Chain: "C" Number of atoms: 1573 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1568 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 10, 'GLN:plan1': 3, 'ASP:plan': 13, 'ASN:plan1': 3, 'HIS:plan': 2, 'TRP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 164 Conformer: "B" Number of residues, atoms: 227, 1568 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 10, 'GLN:plan1': 3, 'ASP:plan': 13, 'ASN:plan1': 3, 'HIS:plan': 2, 'TRP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 164 bond proxies already assigned to first conformer: 1584 Chain: "D" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1439 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 385 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 19, 'ASN:plan1': 4, 'GLN:plan1': 3, 'ARG:plan': 5, 'TRP:plan': 2, 'PHE:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 208 Chain: "E" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2357 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 8, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 447 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASN:plan1': 12, 'GLU:plan': 12, 'ASP:plan': 19, 'ARG:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 171 Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2818 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 14, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 54 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALEU C 47 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLEU C 47 " occ=0.50 Time building chain proxies: 4.57, per 1000 atoms: 0.22 Number of scatterers: 20552 At special positions: 0 Unit cell: (135.24, 146.28, 224.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 3721 8.00 N 3517 7.00 C 13246 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: 1.66 Conformation dependent library (CDL) restraints added in 1.1 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5586 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 12 sheets defined 62.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'A' and resid 53 through 72 removed outlier: 3.601A pdb=" N LYS A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 101 removed outlier: 3.978A pdb=" N SER A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.912A pdb=" N MET A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 151 through 166 Processing helix chain 'A' and resid 178 through 194 Processing helix chain 'A' and resid 197 through 200 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.564A pdb=" N THR A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 249 removed outlier: 8.204A pdb=" N LYS A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.916A pdb=" N LEU A 266 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 289 through 292 removed outlier: 3.609A pdb=" N GLU A 292 " --> pdb=" O VAL A 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 292' Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 322 through 343 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 414 Processing helix chain 'A' and resid 416 through 425 removed outlier: 4.702A pdb=" N VAL A 420 " --> pdb=" O CYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 433 Processing helix chain 'A' and resid 435 through 456 removed outlier: 3.553A pdb=" N ARG A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.564A pdb=" N SER A 513 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN A 514 " --> pdb=" O TRP A 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 510 through 514' Processing helix chain 'A' and resid 520 through 536 removed outlier: 4.380A pdb=" N ILE A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER A 533 " --> pdb=" O HIS A 529 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 4.008A pdb=" N GLY A 540 " --> pdb=" O PRO A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 560 removed outlier: 4.093A pdb=" N LEU A 546 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 580 removed outlier: 3.631A pdb=" N THR A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 591 through 603 removed outlier: 4.003A pdb=" N THR A 595 " --> pdb=" O ASN A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 620 Processing helix chain 'A' and resid 625 through 644 Processing helix chain 'A' and resid 650 through 665 removed outlier: 4.645A pdb=" N ARG A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.562A pdb=" N SER A 669 " --> pdb=" O ASN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 680 Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 695 through 712 Processing helix chain 'A' and resid 727 through 742 Processing helix chain 'A' and resid 747 through 758 Processing helix chain 'A' and resid 759 through 761 No H-bonds generated for 'chain 'A' and resid 759 through 761' Processing helix chain 'A' and resid 762 through 776 removed outlier: 3.546A pdb=" N VAL A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 793 Processing helix chain 'A' and resid 796 through 807 Processing helix chain 'A' and resid 814 through 827 Processing helix chain 'A' and resid 830 through 847 removed outlier: 3.520A pdb=" N LEU A 843 " --> pdb=" O TYR A 839 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 877 removed outlier: 4.346A pdb=" N THR A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 885 removed outlier: 3.754A pdb=" N PHE A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU A 883 " --> pdb=" O GLY A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 895 Processing helix chain 'A' and resid 899 through 917 removed outlier: 5.652A pdb=" N ASP A 909 " --> pdb=" O HIS A 905 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR A 910 " --> pdb=" O ILE A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 951 removed outlier: 3.854A pdb=" N LEU A 951 " --> pdb=" O THR A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.771A pdb=" N ASP A 964 " --> pdb=" O LYS A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 993 Processing helix chain 'A' and resid 993 through 1018 removed outlier: 4.062A pdb=" N GLY A 997 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A1013 " --> pdb=" O GLU A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1034 removed outlier: 4.031A pdb=" N LEU A1031 " --> pdb=" O ILE A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1040 Processing helix chain 'A' and resid 1042 through 1054 removed outlier: 3.546A pdb=" N ALA A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1071 Processing helix chain 'A' and resid 1074 through 1082 removed outlier: 3.520A pdb=" N PHE A1080 " --> pdb=" O LYS A1076 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1107 Processing helix chain 'A' and resid 1113 through 1133 Processing helix chain 'A' and resid 1137 through 1152 removed outlier: 4.014A pdb=" N ILE A1141 " --> pdb=" O ASN A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1155 No H-bonds generated for 'chain 'A' and resid 1153 through 1155' Processing helix chain 'A' and resid 1158 through 1170 Processing helix chain 'A' and resid 1176 through 1187 Proline residue: A1184 - end of helix Processing helix chain 'A' and resid 1205 through 1222 removed outlier: 3.777A pdb=" N GLU A1222 " --> pdb=" O ILE A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 3002 through 3019 Processing helix chain 'B' and resid 3 through 22 removed outlier: 3.791A pdb=" N LEU B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 32 removed outlier: 3.960A pdb=" N HIS B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 39 removed outlier: 3.511A pdb=" N MET B 38 " --> pdb=" O PRO B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.949A pdb=" N PHE B 46 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 47 " --> pdb=" O LEU B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 47' Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.647A pdb=" N HIS B 59 " --> pdb=" O SER B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 78 Processing helix chain 'B' and resid 91 through 106 removed outlier: 3.747A pdb=" N TYR B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 115 through 131 removed outlier: 3.551A pdb=" N LEU B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 Proline residue: B 142 - end of helix Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.881A pdb=" N PHE B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 191 removed outlier: 4.345A pdb=" N LYS B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG B 179 " --> pdb=" O TYR B 175 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 214 removed outlier: 3.504A pdb=" N LEU B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 279 through 320 Proline residue: B 290 - end of helix Processing helix chain 'B' and resid 336 through 341 removed outlier: 3.671A pdb=" N HIS B 341 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 361 Processing helix chain 'B' and resid 378 through 387 Processing helix chain 'B' and resid 392 through 416 removed outlier: 4.072A pdb=" N ASP B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 removed outlier: 3.666A pdb=" N PHE B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 429 " --> pdb=" O CYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 456 Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 470 through 491 removed outlier: 3.910A pdb=" N ASP B 491 " --> pdb=" O THR B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 497 removed outlier: 3.713A pdb=" N PHE B 496 " --> pdb=" O PHE B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 532 Processing helix chain 'B' and resid 577 through 587 Processing helix chain 'C' and resid 8 through 38 removed outlier: 3.739A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 83 Proline residue: C 55 - end of helix removed outlier: 5.540A pdb=" N ASN C 63 " --> pdb=" O ARG C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 removed outlier: 3.656A pdb=" N VAL C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 123 removed outlier: 4.074A pdb=" N ILE C 100 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 121 " --> pdb=" O TYR C 117 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 123 " --> pdb=" O ASN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 removed outlier: 3.564A pdb=" N ILE C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 235 removed outlier: 3.822A pdb=" N VAL C 170 " --> pdb=" O ASP C 166 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 16 removed outlier: 3.668A pdb=" N ILE D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 44 removed outlier: 4.046A pdb=" N LEU D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 102 Processing helix chain 'D' and resid 106 through 143 removed outlier: 4.215A pdb=" N ILE D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG D 136 " --> pdb=" O GLN D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 160 through 169 removed outlier: 3.826A pdb=" N LYS D 165 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 247 removed outlier: 4.693A pdb=" N ILE D 240 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS D 247 " --> pdb=" O GLU D 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 32 Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 200 through 206 removed outlier: 3.695A pdb=" N ILE E 204 " --> pdb=" O ASN E 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 68 removed outlier: 3.519A pdb=" N LEU F 68 " --> pdb=" O LYS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 79 Processing helix chain 'F' and resid 86 through 97 Proline residue: F 94 - end of helix Processing helix chain 'F' and resid 111 through 124 removed outlier: 3.846A pdb=" N VAL F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 154 Processing helix chain 'F' and resid 170 through 180 Processing helix chain 'F' and resid 191 through 201 removed outlier: 3.595A pdb=" N GLU F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 223 Processing helix chain 'F' and resid 223 through 236 removed outlier: 3.576A pdb=" N ALA F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'F' and resid 292 through 304 removed outlier: 3.794A pdb=" N ASP F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 329 Processing helix chain 'F' and resid 341 through 354 Processing helix chain 'F' and resid 364 through 367 Processing helix chain 'F' and resid 386 through 395 Processing helix chain 'F' and resid 412 through 427 removed outlier: 3.970A pdb=" N GLN F 423 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 424 " --> pdb=" O ALA F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 471 through 475 Processing sheet with id=AA2, first strand: chain 'A' and resid 484 through 485 removed outlier: 6.889A pdb=" N ARG A 484 " --> pdb=" O TYR C 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 491 removed outlier: 3.640A pdb=" N SER A 497 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 66 through 71 removed outlier: 6.721A pdb=" N SER E 81 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU E 69 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA E 79 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL E 101 " --> pdb=" O PHE E 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 117 through 119 removed outlier: 3.553A pdb=" N ASP E 117 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU E 141 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS E 151 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 163 through 168 removed outlier: 6.740A pdb=" N ALA E 178 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N CYS E 166 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU E 176 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR E 168 " --> pdb=" O TRP E 174 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP E 174 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP E 188 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER E 195 " --> pdb=" O ASP E 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 214 through 217 removed outlier: 6.259A pdb=" N LYS E 237 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL E 245 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 256 through 261 removed outlier: 4.403A pdb=" N CYS E 277 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E 289 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN E 281 " --> pdb=" O CYS E 287 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N CYS E 287 " --> pdb=" O ASN E 281 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 298 through 303 removed outlier: 3.547A pdb=" N THR E 300 " --> pdb=" O CYS E 313 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP E 323 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU E 329 " --> pdb=" O ASP E 323 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 344 through 346 Processing sheet with id=AB2, first strand: chain 'F' and resid 102 through 104 removed outlier: 6.135A pdb=" N VAL F 102 " --> pdb=" O MET F 245 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE F 212 " --> pdb=" O MET F 244 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE F 246 " --> pdb=" O PHE F 212 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE F 214 " --> pdb=" O PHE F 246 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL F 134 " --> pdb=" O VAL F 213 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASP F 215 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE F 136 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA F 163 " --> pdb=" O VAL F 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 333 through 336 removed outlier: 6.209A pdb=" N VAL F 309 " --> pdb=" O CYS F 360 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N SER F 362 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ILE F 311 " --> pdb=" O SER F 362 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN F 308 " --> pdb=" O LEU F 377 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE F 379 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE F 310 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN F 282 " --> pdb=" O ALA F 406 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N SER F 408 " --> pdb=" O GLN F 282 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TYR F 284 " --> pdb=" O SER F 408 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL F 410 " --> pdb=" O TYR F 284 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE F 286 " --> pdb=" O VAL F 410 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA F 431 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR F 285 " --> pdb=" O ALA F 431 " (cutoff:3.500A) 1290 hydrogen bonds defined for protein. 3798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 2.37 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: 4444 1.33 - 1.45: 4536 1.45 - 1.57: 11871 1.57 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 20956 Sorted by residual: bond pdb=" C ILE A 990 " pdb=" O ILE A 990 " ideal model delta sigma weight residual 1.236 1.277 -0.041 1.19e-02 7.06e+03 1.20e+01 bond pdb=" N GLU A 31 " pdb=" CA GLU A 31 " ideal model delta sigma weight residual 1.453 1.493 -0.040 1.31e-02 5.83e+03 9.26e+00 bond pdb=" N GLU B 544 " pdb=" CA GLU B 544 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.27e-02 6.20e+03 9.06e+00 bond pdb=" N ILE A 993 " pdb=" CA ILE A 993 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.55e+00 bond pdb=" N VAL B 545 " pdb=" CA VAL B 545 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.64e+00 ... (remaining 20951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 27686 1.86 - 3.72: 807 3.72 - 5.58: 130 5.58 - 7.43: 18 7.43 - 9.29: 5 Bond angle restraints: 28646 Sorted by residual: angle pdb=" N PRO A1156 " pdb=" CA PRO A1156 " pdb=" CB PRO A1156 " ideal model delta sigma weight residual 102.25 110.18 -7.93 7.00e-01 2.04e+00 1.28e+02 angle pdb=" N ASN A 36 " pdb=" CA ASN A 36 " pdb=" C ASN A 36 " ideal model delta sigma weight residual 112.58 103.29 9.29 1.22e+00 6.72e-01 5.80e+01 angle pdb=" N ILE A 34 " pdb=" CA ILE A 34 " pdb=" C ILE A 34 " ideal model delta sigma weight residual 113.00 105.05 7.95 1.30e+00 5.92e-01 3.74e+01 angle pdb=" CA ILE A 993 " pdb=" C ILE A 993 " pdb=" O ILE A 993 " ideal model delta sigma weight residual 120.78 114.15 6.63 1.25e+00 6.40e-01 2.81e+01 angle pdb=" CA ASP B 441 " pdb=" C ASP B 441 " pdb=" O ASP B 441 " ideal model delta sigma weight residual 120.82 115.64 5.18 1.05e+00 9.07e-01 2.43e+01 ... (remaining 28641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10958 17.92 - 35.84: 1065 35.84 - 53.76: 311 53.76 - 71.68: 49 71.68 - 89.60: 17 Dihedral angle restraints: 12400 sinusoidal: 3840 harmonic: 8560 Sorted by residual: dihedral pdb=" CA PHE A 932 " pdb=" C PHE A 932 " pdb=" N SER A 933 " pdb=" CA SER A 933 " ideal model delta harmonic sigma weight residual -180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA SER D 47 " pdb=" C SER D 47 " pdb=" N ASN D 48 " pdb=" CA ASN D 48 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA GLU E 65 " pdb=" C GLU E 65 " pdb=" N ILE E 66 " pdb=" CA ILE E 66 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 12397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2753 0.053 - 0.105: 600 0.105 - 0.158: 94 0.158 - 0.210: 15 0.210 - 0.263: 6 Chirality restraints: 3468 Sorted by residual: chirality pdb=" CA ILE A 34 " pdb=" N ILE A 34 " pdb=" C ILE A 34 " pdb=" CB ILE A 34 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA VAL A 17 " pdb=" N VAL A 17 " pdb=" C VAL A 17 " pdb=" CB VAL A 17 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA VAL A 33 " pdb=" N VAL A 33 " pdb=" C VAL A 33 " pdb=" CB VAL A 33 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3465 not shown) Planarity restraints: 3656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 932 " 0.020 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C PHE A 932 " -0.067 2.00e-02 2.50e+03 pdb=" O PHE A 932 " 0.025 2.00e-02 2.50e+03 pdb=" N SER A 933 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1194 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ALA A1194 " 0.057 2.00e-02 2.50e+03 pdb=" O ALA A1194 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG A1195 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 887 " 0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO A 888 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 888 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 888 " 0.033 5.00e-02 4.00e+02 ... (remaining 3653 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 269 2.65 - 3.21: 20338 3.21 - 3.78: 30866 3.78 - 4.34: 37829 4.34 - 4.90: 63539 Nonbonded interactions: 152841 Sorted by model distance: nonbonded pdb=" O LEU A 524 " pdb=" OG SER A 528 " model vdw 2.090 3.040 nonbonded pdb=" NH1 ARG B 313 " pdb=" OD1 ASP C 127 " model vdw 2.092 3.120 nonbonded pdb=" O ASP F 439 " pdb=" OG1 THR F 442 " model vdw 2.163 3.040 nonbonded pdb=" O ARG A 820 " pdb=" OG SER A 823 " model vdw 2.176 3.040 nonbonded pdb=" OD1 ASP B 258 " pdb=" OG SER B 287 " model vdw 2.177 3.040 ... (remaining 152836 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.200 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 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 : 0.006 0.041 20956 Z= 0.286 Angle : 0.765 9.292 28646 Z= 0.472 Chirality : 0.046 0.263 3468 Planarity : 0.004 0.060 3656 Dihedral : 16.323 89.603 6814 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.28 % Favored : 93.61 % Rotamer: Outliers : 9.74 % Allowed : 20.04 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.30 (0.14), residues: 2837 helix: -0.68 (0.12), residues: 1634 sheet: -1.05 (0.33), residues: 231 loop : -3.05 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 239 TYR 0.016 0.002 TYR B 280 PHE 0.029 0.002 PHE A 694 TRP 0.016 0.002 TRP A 316 HIS 0.005 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00596 (20956) covalent geometry : angle 0.76491 (28646) hydrogen bonds : bond 0.14419 ( 1290) hydrogen bonds : angle 6.04616 ( 3798) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 144 time to evaluate : 0.841 Fit side-chains REVERT: A 93 LEU cc_start: 0.9007 (mt) cc_final: 0.8787 (mt) REVERT: A 136 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.8040 (m90) REVERT: A 285 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7799 (p90) REVERT: A 298 MET cc_start: 0.9084 (tpp) cc_final: 0.8693 (tpp) REVERT: A 331 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7746 (mp-120) REVERT: A 498 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8613 (tt) REVERT: A 1041 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8387 (m-80) REVERT: A 1148 MET cc_start: 0.9158 (mmm) cc_final: 0.8814 (mmp) REVERT: B 258 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8068 (t0) REVERT: B 367 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8894 (tt) REVERT: B 376 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9133 (mt) REVERT: B 429 GLU cc_start: 0.8012 (pt0) cc_final: 0.7589 (pp20) REVERT: C 18 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8723 (tp-100) REVERT: C 107 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.7713 (t80) REVERT: C 146 LYS cc_start: 0.9242 (mmtt) cc_final: 0.9032 (mmtp) REVERT: C 176 ASN cc_start: 0.8591 (m-40) cc_final: 0.8142 (t0) REVERT: C 188 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.6878 (t80) REVERT: D 29 ASP cc_start: 0.9342 (t0) cc_final: 0.9035 (t0) REVERT: E 318 MET cc_start: 0.7767 (ttm) cc_final: 0.7349 (ttm) REVERT: E 373 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8446 (tp) REVERT: F 244 MET cc_start: -0.1767 (mpp) cc_final: -0.2095 (mpp) outliers start: 174 outliers final: 78 residues processed: 313 average time/residue: 0.1285 time to fit residues: 65.4365 Evaluate side-chains 208 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 119 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 366 PHE Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 256 HIS A 262 ASN A 318 ASN ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS A 529 HIS ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 ASN A1032 GLN A1033 ASN B 221 ASN B 350 ASN B 388 GLN C 79 GLN D 25 ASN D 114 HIS ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 HIS E 252 HIS E 281 ASN F 122 GLN F 123 GLN ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 ASN F 423 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.100525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.062971 restraints weight = 90161.167| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.97 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20956 Z= 0.215 Angle : 0.623 8.112 28646 Z= 0.332 Chirality : 0.043 0.171 3468 Planarity : 0.004 0.052 3656 Dihedral : 8.241 79.736 3205 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 6.77 % Allowed : 21.95 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.16), residues: 2837 helix: 0.79 (0.13), residues: 1665 sheet: -0.76 (0.33), residues: 239 loop : -2.42 (0.18), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 551 TYR 0.015 0.002 TYR F 390 PHE 0.027 0.002 PHE A 694 TRP 0.012 0.001 TRP A1018 HIS 0.004 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00506 (20956) covalent geometry : angle 0.62280 (28646) hydrogen bonds : bond 0.05735 ( 1290) hydrogen bonds : angle 4.49695 ( 3798) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 129 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 485 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8686 (mt) REVERT: A 791 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8441 (mt) REVERT: A 1094 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.6495 (t80) REVERT: A 1148 MET cc_start: 0.8912 (mmm) cc_final: 0.8578 (mmp) REVERT: B 195 ASN cc_start: 0.9311 (OUTLIER) cc_final: 0.9075 (m-40) REVERT: B 214 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7607 (mt) REVERT: B 258 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8148 (t70) REVERT: B 318 GLU cc_start: 0.8423 (tp30) cc_final: 0.7988 (tp30) REVERT: B 367 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.8834 (tt) REVERT: B 442 GLU cc_start: 0.8300 (tp30) cc_final: 0.8072 (tp30) REVERT: B 449 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7571 (mt) REVERT: C 107 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7248 (t80) REVERT: C 108 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8735 (mt-10) REVERT: C 176 ASN cc_start: 0.8395 (m-40) cc_final: 0.7950 (t0) REVERT: C 188 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6781 (t80) REVERT: D 29 ASP cc_start: 0.9487 (t0) cc_final: 0.9122 (t0) REVERT: D 87 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8395 (tm-30) REVERT: D 95 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8867 (tm-30) REVERT: D 132 GLN cc_start: 0.8428 (tp40) cc_final: 0.7375 (tm-30) REVERT: E 318 MET cc_start: 0.7874 (ttm) cc_final: 0.7305 (ttm) REVERT: F 244 MET cc_start: -0.0965 (mpp) cc_final: -0.1364 (mpp) outliers start: 121 outliers final: 70 residues processed: 242 average time/residue: 0.1229 time to fit residues: 49.6388 Evaluate side-chains 197 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 117 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 893 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 366 PHE Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 360 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 144 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 208 optimal weight: 30.0000 chunk 93 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 167 optimal weight: 0.0170 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 ASN B 397 GLN E 29 GLN ** F 186 HIS ** 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 = 0.3683 r_free = 0.3683 target = 0.099562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.062574 restraints weight = 73166.158| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.57 r_work: 0.2744 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20956 Z= 0.250 Angle : 0.642 8.714 28646 Z= 0.341 Chirality : 0.043 0.171 3468 Planarity : 0.004 0.051 3656 Dihedral : 7.423 59.020 3136 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 7.50 % Allowed : 22.45 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.16), residues: 2837 helix: 1.19 (0.13), residues: 1669 sheet: -0.57 (0.33), residues: 237 loop : -2.20 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 313 TYR 0.015 0.002 TYR A 839 PHE 0.028 0.002 PHE A 694 TRP 0.013 0.002 TRP A1018 HIS 0.005 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00594 (20956) covalent geometry : angle 0.64175 (28646) hydrogen bonds : bond 0.05868 ( 1290) hydrogen bonds : angle 4.38668 ( 3798) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 125 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 110 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8897 (t80) REVERT: A 331 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7635 (mp-120) REVERT: A 485 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8442 (mt) REVERT: A 714 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.6657 (ptp-170) REVERT: A 791 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8474 (mt) REVERT: A 817 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8071 (pt) REVERT: A 1094 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.6575 (t80) REVERT: A 1139 MET cc_start: 0.8026 (mmt) cc_final: 0.7724 (mmt) REVERT: A 1148 MET cc_start: 0.8725 (mmm) cc_final: 0.8446 (mmp) REVERT: B 98 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8852 (mp) REVERT: B 153 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8428 (ptm) REVERT: B 195 ASN cc_start: 0.9331 (OUTLIER) cc_final: 0.9065 (m-40) REVERT: B 214 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7797 (mt) REVERT: B 258 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8293 (t0) REVERT: B 318 GLU cc_start: 0.8576 (tp30) cc_final: 0.8302 (tp30) REVERT: B 357 GLN cc_start: 0.8420 (tp40) cc_final: 0.8153 (tp40) REVERT: B 367 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9020 (tt) REVERT: B 387 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8718 (p) REVERT: B 449 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7511 (mt) REVERT: B 519 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8712 (t) REVERT: C 107 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.6867 (t80) REVERT: C 108 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8811 (mt-10) REVERT: C 176 ASN cc_start: 0.8249 (m-40) cc_final: 0.7817 (t0) REVERT: D 29 ASP cc_start: 0.9453 (t0) cc_final: 0.9124 (t0) REVERT: D 95 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8921 (tm-30) REVERT: D 132 GLN cc_start: 0.8460 (tp40) cc_final: 0.7363 (tm-30) REVERT: D 133 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7802 (p) REVERT: E 302 ASP cc_start: 0.8358 (t70) cc_final: 0.8112 (t70) REVERT: E 318 MET cc_start: 0.7977 (ttm) cc_final: 0.7474 (ttm) REVERT: F 244 MET cc_start: -0.0134 (mpp) cc_final: -0.0745 (mpp) outliers start: 134 outliers final: 83 residues processed: 247 average time/residue: 0.1227 time to fit residues: 49.5498 Evaluate side-chains 221 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 120 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 366 PHE Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 360 CYS Chi-restraints excluded: chain F residue 430 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 252 optimal weight: 20.0000 chunk 121 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 226 optimal weight: 8.9990 chunk 229 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 264 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 ASN ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.100951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.063405 restraints weight = 84046.035| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.85 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20956 Z= 0.172 Angle : 0.571 8.677 28646 Z= 0.302 Chirality : 0.041 0.161 3468 Planarity : 0.003 0.043 3656 Dihedral : 6.796 58.547 3120 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 6.33 % Allowed : 23.85 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.16), residues: 2837 helix: 1.56 (0.13), residues: 1661 sheet: -0.41 (0.33), residues: 237 loop : -2.04 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 313 TYR 0.026 0.001 TYR F 349 PHE 0.023 0.001 PHE A 694 TRP 0.014 0.001 TRP A1018 HIS 0.003 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00400 (20956) covalent geometry : angle 0.57055 (28646) hydrogen bonds : bond 0.05066 ( 1290) hydrogen bonds : angle 4.09692 ( 3798) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 130 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8984 (t80) REVERT: A 331 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7516 (mp-120) REVERT: A 333 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8260 (tt) REVERT: A 791 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8474 (mt) REVERT: A 817 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.8018 (pt) REVERT: A 861 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7847 (tp30) REVERT: A 1094 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.6488 (t80) REVERT: A 1139 MET cc_start: 0.8102 (mmt) cc_final: 0.7834 (mmt) REVERT: A 1148 MET cc_start: 0.8921 (mmm) cc_final: 0.8524 (mmp) REVERT: B 94 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8662 (tm) REVERT: B 98 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8786 (mp) REVERT: B 153 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8342 (ptm) REVERT: B 195 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8964 (m-40) REVERT: B 258 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8284 (t0) REVERT: B 318 GLU cc_start: 0.8458 (tp30) cc_final: 0.8121 (tp30) REVERT: B 345 MET cc_start: 0.7299 (mtm) cc_final: 0.7085 (ptm) REVERT: B 357 GLN cc_start: 0.8368 (tp40) cc_final: 0.8074 (tp40) REVERT: B 367 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9082 (tt) REVERT: B 387 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8647 (p) REVERT: C 107 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.6765 (t80) REVERT: C 108 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8897 (mt-10) REVERT: C 176 ASN cc_start: 0.8435 (m-40) cc_final: 0.7996 (t0) REVERT: C 188 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6676 (t80) REVERT: D 29 ASP cc_start: 0.9446 (t0) cc_final: 0.9089 (t0) REVERT: D 95 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8845 (tm-30) REVERT: D 132 GLN cc_start: 0.8330 (tp40) cc_final: 0.7258 (tm-30) REVERT: E 302 ASP cc_start: 0.8177 (t70) cc_final: 0.7883 (t70) REVERT: F 244 MET cc_start: -0.0895 (mpp) cc_final: -0.1096 (mmm) REVERT: F 392 HIS cc_start: 0.8633 (m170) cc_final: 0.8378 (m170) outliers start: 113 outliers final: 77 residues processed: 232 average time/residue: 0.1189 time to fit residues: 45.6220 Evaluate side-chains 219 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 126 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 360 CYS Chi-restraints excluded: chain F residue 430 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 146 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 135 optimal weight: 0.4980 chunk 110 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 279 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 ASN ** F 186 HIS ** 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 = 0.3708 r_free = 0.3708 target = 0.101457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.062141 restraints weight = 108454.393| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 4.54 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20956 Z= 0.158 Angle : 0.553 8.286 28646 Z= 0.292 Chirality : 0.041 0.154 3468 Planarity : 0.003 0.040 3656 Dihedral : 6.354 58.427 3112 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.15 % Favored : 94.81 % Rotamer: Outliers : 6.83 % Allowed : 23.40 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.68 (0.16), residues: 2837 helix: 1.81 (0.13), residues: 1660 sheet: -0.17 (0.34), residues: 240 loop : -1.96 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 313 TYR 0.018 0.001 TYR F 349 PHE 0.021 0.001 PHE A 694 TRP 0.013 0.001 TRP A1018 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00365 (20956) covalent geometry : angle 0.55335 (28646) hydrogen bonds : bond 0.04747 ( 1290) hydrogen bonds : angle 3.96255 ( 3798) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 128 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8975 (t80) REVERT: A 331 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7471 (mp-120) REVERT: A 333 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8192 (tt) REVERT: A 587 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8767 (tt) REVERT: A 791 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8455 (mt) REVERT: A 817 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7975 (pt) REVERT: A 861 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: A 1094 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.6378 (t80) REVERT: A 1139 MET cc_start: 0.8012 (mmt) cc_final: 0.7770 (mmt) REVERT: A 1148 MET cc_start: 0.8862 (mmm) cc_final: 0.8452 (mmp) REVERT: B 153 MET cc_start: 0.8495 (ptm) cc_final: 0.8146 (ptm) REVERT: B 318 GLU cc_start: 0.8423 (tp30) cc_final: 0.8040 (tp30) REVERT: B 357 GLN cc_start: 0.8311 (tp40) cc_final: 0.8050 (tp40) REVERT: B 367 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9060 (tt) REVERT: B 387 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8533 (p) REVERT: C 107 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.6615 (t80) REVERT: C 108 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8881 (mt-10) REVERT: C 188 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6577 (t80) REVERT: C 191 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7187 (tm-30) REVERT: D 29 ASP cc_start: 0.9443 (t0) cc_final: 0.9077 (t0) REVERT: D 95 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8848 (tm-30) REVERT: D 132 GLN cc_start: 0.8268 (tp40) cc_final: 0.7189 (tm-30) REVERT: E 302 ASP cc_start: 0.8199 (t70) cc_final: 0.7871 (t70) REVERT: E 318 MET cc_start: 0.8383 (mmm) cc_final: 0.8131 (tpp) REVERT: F 392 HIS cc_start: 0.8706 (m170) cc_final: 0.8502 (m170) outliers start: 122 outliers final: 90 residues processed: 238 average time/residue: 0.1193 time to fit residues: 47.9338 Evaluate side-chains 227 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 125 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1150 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 360 CYS Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 430 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 chunk 280 optimal weight: 40.0000 chunk 155 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 162 optimal weight: 0.0770 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 ASN A 957 HIS B 221 ASN B 397 GLN ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.102878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.063810 restraints weight = 100933.884| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 4.39 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20956 Z= 0.121 Angle : 0.521 9.160 28646 Z= 0.273 Chirality : 0.039 0.146 3468 Planarity : 0.003 0.038 3656 Dihedral : 5.840 59.187 3106 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.17 % Rotamer: Outliers : 5.60 % Allowed : 24.80 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.17), residues: 2837 helix: 1.97 (0.13), residues: 1682 sheet: -0.14 (0.34), residues: 234 loop : -1.84 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 295 TYR 0.025 0.001 TYR F 349 PHE 0.018 0.001 PHE A 694 TRP 0.013 0.001 TRP A1018 HIS 0.002 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00269 (20956) covalent geometry : angle 0.52121 (28646) hydrogen bonds : bond 0.04111 ( 1290) hydrogen bonds : angle 3.76884 ( 3798) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 130 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7473 (mp-120) REVERT: A 791 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8449 (mt) REVERT: A 861 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7514 (tp30) REVERT: A 1094 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.6532 (t80) REVERT: A 1139 MET cc_start: 0.7936 (mmt) cc_final: 0.7706 (mmt) REVERT: A 1148 MET cc_start: 0.8912 (mmm) cc_final: 0.8438 (mmp) REVERT: B 195 ASN cc_start: 0.9173 (OUTLIER) cc_final: 0.8706 (m-40) REVERT: B 318 GLU cc_start: 0.8360 (tp30) cc_final: 0.7976 (tp30) REVERT: B 357 GLN cc_start: 0.8356 (tp40) cc_final: 0.8089 (tp40) REVERT: B 367 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.8998 (tt) REVERT: B 387 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8435 (p) REVERT: C 107 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.6625 (t80) REVERT: C 108 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8873 (mt-10) REVERT: C 188 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6621 (t80) REVERT: D 29 ASP cc_start: 0.9390 (t0) cc_final: 0.9055 (t0) REVERT: D 95 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8909 (tm-30) REVERT: D 132 GLN cc_start: 0.8121 (tp40) cc_final: 0.7117 (tm-30) REVERT: D 133 VAL cc_start: 0.8121 (OUTLIER) cc_final: 0.7914 (p) REVERT: E 302 ASP cc_start: 0.8173 (t70) cc_final: 0.7809 (t70) REVERT: E 318 MET cc_start: 0.8435 (mmm) cc_final: 0.8199 (tpp) REVERT: F 284 TYR cc_start: 0.5668 (m-80) cc_final: 0.5155 (t80) REVERT: F 392 HIS cc_start: 0.8711 (m170) cc_final: 0.8493 (m170) outliers start: 100 outliers final: 69 residues processed: 221 average time/residue: 0.1234 time to fit residues: 44.9067 Evaluate side-chains 201 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 122 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1150 HIS Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 360 CYS Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 430 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 148 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 202 optimal weight: 0.7980 chunk 258 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN E 72 HIS ** F 186 HIS ** 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 = 0.3687 r_free = 0.3687 target = 0.100202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.061281 restraints weight = 90753.335| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 4.16 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20956 Z= 0.226 Angle : 0.611 10.090 28646 Z= 0.321 Chirality : 0.042 0.163 3468 Planarity : 0.004 0.038 3656 Dihedral : 5.969 59.841 3100 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 6.27 % Allowed : 24.47 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.80 (0.17), residues: 2837 helix: 1.83 (0.13), residues: 1681 sheet: 0.03 (0.34), residues: 241 loop : -1.88 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 76 TYR 0.026 0.002 TYR F 349 PHE 0.026 0.002 PHE A 694 TRP 0.010 0.001 TRP B 532 HIS 0.003 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00536 (20956) covalent geometry : angle 0.61105 (28646) hydrogen bonds : bond 0.05285 ( 1290) hydrogen bonds : angle 4.03723 ( 3798) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 124 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7676 (mp-120) REVERT: A 714 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.6981 (ptt90) REVERT: A 791 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8461 (mt) REVERT: A 1055 MET cc_start: 0.8460 (tmm) cc_final: 0.8195 (tmm) REVERT: A 1094 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.6457 (t80) REVERT: A 1139 MET cc_start: 0.8106 (mmt) cc_final: 0.7687 (mmt) REVERT: B 168 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8293 (mm) REVERT: B 195 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.8949 (m-40) REVERT: B 214 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7500 (mt) REVERT: B 296 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8334 (mp) REVERT: B 318 GLU cc_start: 0.8410 (tp30) cc_final: 0.7994 (tp30) REVERT: B 357 GLN cc_start: 0.8422 (tp40) cc_final: 0.8164 (tp40) REVERT: B 367 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.8942 (tt) REVERT: B 387 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8690 (p) REVERT: C 107 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.6711 (t80) REVERT: D 29 ASP cc_start: 0.9485 (t0) cc_final: 0.9136 (t0) REVERT: D 95 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8889 (tm-30) REVERT: E 302 ASP cc_start: 0.8173 (t70) cc_final: 0.7890 (t70) REVERT: E 318 MET cc_start: 0.8514 (mmm) cc_final: 0.8271 (tpp) REVERT: F 392 HIS cc_start: 0.8767 (m170) cc_final: 0.8548 (m170) outliers start: 112 outliers final: 89 residues processed: 228 average time/residue: 0.1199 time to fit residues: 45.7630 Evaluate side-chains 222 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 122 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 360 CYS Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 444 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 66 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 236 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 276 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 269 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 ASN B 221 ASN F 186 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.101182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.062153 restraints weight = 98569.629| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 4.34 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20956 Z= 0.168 Angle : 0.565 10.617 28646 Z= 0.295 Chirality : 0.041 0.152 3468 Planarity : 0.003 0.039 3656 Dihedral : 5.848 59.768 3100 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.19 % Favored : 94.78 % Rotamer: Outliers : 5.88 % Allowed : 25.42 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.17), residues: 2837 helix: 1.97 (0.13), residues: 1669 sheet: 0.06 (0.34), residues: 245 loop : -1.85 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 295 TYR 0.022 0.001 TYR F 349 PHE 0.021 0.001 PHE A 694 TRP 0.012 0.001 TRP A1018 HIS 0.002 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00392 (20956) covalent geometry : angle 0.56462 (28646) hydrogen bonds : bond 0.04715 ( 1290) hydrogen bonds : angle 3.89438 ( 3798) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 124 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7237 (tm-30) REVERT: A 139 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8701 (mt) REVERT: A 331 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7553 (mp-120) REVERT: A 791 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8530 (mt) REVERT: A 861 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7773 (tp30) REVERT: A 1055 MET cc_start: 0.8491 (tmm) cc_final: 0.8244 (tmm) REVERT: A 1094 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.6456 (t80) REVERT: A 1139 MET cc_start: 0.8149 (mmt) cc_final: 0.7846 (mmt) REVERT: A 1148 MET cc_start: 0.8844 (mmm) cc_final: 0.8294 (mmp) REVERT: B 195 ASN cc_start: 0.9243 (OUTLIER) cc_final: 0.8924 (m-40) REVERT: B 214 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7492 (mt) REVERT: B 296 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8309 (mp) REVERT: B 318 GLU cc_start: 0.8403 (tp30) cc_final: 0.7985 (tp30) REVERT: B 357 GLN cc_start: 0.8443 (tp40) cc_final: 0.8181 (tp40) REVERT: B 367 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.8947 (tt) REVERT: B 387 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8624 (p) REVERT: C 107 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.6699 (t80) REVERT: C 108 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8835 (mt-10) REVERT: D 29 ASP cc_start: 0.9420 (t0) cc_final: 0.9093 (t0) REVERT: D 95 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8901 (tm-30) REVERT: E 302 ASP cc_start: 0.8118 (t70) cc_final: 0.7791 (t70) REVERT: E 318 MET cc_start: 0.8485 (mmm) cc_final: 0.8256 (tpp) REVERT: F 392 HIS cc_start: 0.8777 (m170) cc_final: 0.8560 (m170) outliers start: 105 outliers final: 83 residues processed: 221 average time/residue: 0.1177 time to fit residues: 43.1660 Evaluate side-chains 217 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 123 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1150 HIS Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 360 CYS Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 430 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 182 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 199 optimal weight: 5.9990 chunk 283 optimal weight: 0.0570 chunk 242 optimal weight: 0.2980 chunk 280 optimal weight: 50.0000 chunk 226 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 GLN A 794 ASN E 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.103768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.064744 restraints weight = 89894.299| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 4.23 r_work: 0.2828 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20956 Z= 0.106 Angle : 0.522 10.879 28646 Z= 0.272 Chirality : 0.039 0.155 3468 Planarity : 0.003 0.041 3656 Dihedral : 5.530 59.669 3098 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.75 % Allowed : 27.38 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.17), residues: 2837 helix: 2.20 (0.13), residues: 1673 sheet: 0.25 (0.35), residues: 244 loop : -1.79 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 313 TYR 0.020 0.001 TYR F 349 PHE 0.017 0.001 PHE B 222 TRP 0.017 0.001 TRP A1018 HIS 0.003 0.000 HIS A 957 Details of bonding type rmsd covalent geometry : bond 0.00220 (20956) covalent geometry : angle 0.52156 (28646) hydrogen bonds : bond 0.03738 ( 1290) hydrogen bonds : angle 3.65435 ( 3798) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 131 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7351 (tm-30) cc_final: 0.7079 (tm-30) REVERT: A 791 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8482 (mt) REVERT: A 861 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: A 1094 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.6606 (t80) REVERT: B 195 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8745 (m-40) REVERT: B 357 GLN cc_start: 0.8504 (tp40) cc_final: 0.8287 (tp40) REVERT: B 367 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.8938 (tt) REVERT: B 387 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8543 (p) REVERT: C 107 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.6846 (t80) REVERT: C 108 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8963 (mt-10) REVERT: D 29 ASP cc_start: 0.9257 (t0) cc_final: 0.8972 (t0) REVERT: D 95 GLU cc_start: 0.9219 (tm-30) cc_final: 0.9018 (tm-30) REVERT: E 302 ASP cc_start: 0.8231 (t70) cc_final: 0.7876 (t70) REVERT: E 318 MET cc_start: 0.8550 (mmm) cc_final: 0.8334 (tpp) outliers start: 67 outliers final: 55 residues processed: 193 average time/residue: 0.1250 time to fit residues: 39.3869 Evaluate side-chains 187 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 125 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1150 HIS Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 360 CYS Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 430 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 265 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 chunk 192 optimal weight: 50.0000 chunk 164 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 414 HIS ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.102225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.062473 restraints weight = 95796.417| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 4.44 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20956 Z= 0.217 Angle : 0.615 13.259 28646 Z= 0.320 Chirality : 0.042 0.148 3468 Planarity : 0.004 0.039 3656 Dihedral : 5.575 59.969 3088 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.09 % Allowed : 27.10 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.03 (0.17), residues: 2837 helix: 2.04 (0.13), residues: 1665 sheet: 0.08 (0.34), residues: 248 loop : -1.78 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 76 TYR 0.016 0.001 TYR F 349 PHE 0.024 0.002 PHE A 694 TRP 0.011 0.001 TRP B 532 HIS 0.003 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00515 (20956) covalent geometry : angle 0.61463 (28646) hydrogen bonds : bond 0.05138 ( 1290) hydrogen bonds : angle 3.95302 ( 3798) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 121 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 791 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8273 (mt) REVERT: A 861 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7786 (tp30) REVERT: A 1094 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.6292 (t80) REVERT: B 195 ASN cc_start: 0.9262 (OUTLIER) cc_final: 0.8760 (m-40) REVERT: B 296 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8067 (mp) REVERT: B 318 GLU cc_start: 0.8664 (tp30) cc_final: 0.8119 (tp30) REVERT: B 357 GLN cc_start: 0.8282 (tp40) cc_final: 0.8037 (tp40) REVERT: B 367 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8877 (tt) REVERT: B 387 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8457 (p) REVERT: C 18 GLN cc_start: 0.8670 (mt0) cc_final: 0.8426 (mt0) REVERT: C 107 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.6558 (t80) REVERT: C 108 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8798 (mt-10) REVERT: D 29 ASP cc_start: 0.9341 (t0) cc_final: 0.9045 (t0) REVERT: D 95 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8845 (tm-30) REVERT: E 302 ASP cc_start: 0.8048 (t70) cc_final: 0.7635 (t70) REVERT: E 318 MET cc_start: 0.8416 (mmm) cc_final: 0.8160 (tpp) outliers start: 73 outliers final: 60 residues processed: 189 average time/residue: 0.1182 time to fit residues: 36.7977 Evaluate side-chains 189 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 121 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 430 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 175 optimal weight: 0.4980 chunk 111 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 276 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN A 794 ASN ** B 195 ASN ** 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 = 0.3711 r_free = 0.3711 target = 0.102591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.063287 restraints weight = 83312.812| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.15 r_work: 0.2791 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20956 Z= 0.186 Angle : 0.585 12.690 28646 Z= 0.304 Chirality : 0.041 0.149 3468 Planarity : 0.003 0.038 3656 Dihedral : 5.548 58.895 3086 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.54 % Allowed : 26.48 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.17), residues: 2837 helix: 2.05 (0.13), residues: 1668 sheet: 0.12 (0.34), residues: 245 loop : -1.77 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 76 TYR 0.016 0.001 TYR F 349 PHE 0.021 0.001 PHE A 694 TRP 0.010 0.001 TRP B 532 HIS 0.003 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00440 (20956) covalent geometry : angle 0.58511 (28646) hydrogen bonds : bond 0.04805 ( 1290) hydrogen bonds : angle 3.89337 ( 3798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5639.73 seconds wall clock time: 96 minutes 48.87 seconds (5808.87 seconds total)