Starting phenix.real_space_refine on Sun Feb 18 02:53:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apx_11859/02_2024/7apx_11859.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apx_11859/02_2024/7apx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apx_11859/02_2024/7apx_11859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apx_11859/02_2024/7apx_11859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apx_11859/02_2024/7apx_11859.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apx_11859/02_2024/7apx_11859.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A ARG 637": "NH1" <-> "NH2" Residue "A GLU 638": "OE1" <-> "OE2" Residue "A ARG 656": "NH1" <-> "NH2" Residue "A ARG 709": "NH1" <-> "NH2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A GLU 861": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E ARG 266": "NH1" <-> "NH2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "F ARG 228": "NH1" <-> "NH2" Residue "F GLU 292": "OE1" <-> "OE2" Residue "F GLU 343": "OE1" <-> "OE2" Residue "F GLU 344": "OE1" <-> "OE2" Residue "F GLU 414": "OE1" <-> "OE2" Residue "F GLU 424": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20552 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 8222 Classifications: {'peptide': 1165} Incomplete info: {'truncation_to_alanine': 375} Link IDs: {'PTRANS': 33, 'TRANS': 1131} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1255 Unresolved non-hydrogen angles: 1575 Unresolved non-hydrogen dihedrals: 988 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 5, 'UNK:plan-1': 19, 'TYR:plan': 4, 'ASN:plan1': 30, 'TRP:plan': 2, 'ASP:plan': 36, 'PHE:plan': 7, 'GLU:plan': 63, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 741 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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 15, 'ASP:plan': 24, 'PHE:plan': 2, 'GLU:plan': 35, 'ARG:plan': 10} 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: {'GLN:plan1': 3, 'ASP:plan': 13, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6} 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: {'GLN:plan1': 3, 'ASP:plan': 13, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6} 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: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'ASP:plan': 19, 'TYR:plan': 1, 'ASN:plan1': 12, 'HIS:plan': 2, 'GLU:plan': 12, 'ARG: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: {'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} 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: 11.90, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.17 Conformation dependent library (CDL) restraints added in 4.3 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: 2.30 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: 6.61 Time building geometry restraints manager: 8.79 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: 99.30 - 106.28: 412 106.28 - 113.25: 11744 113.25 - 120.23: 7642 120.23 - 127.20: 8659 127.20 - 134.18: 189 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 2.440 nonbonded pdb=" NH1 ARG B 313 " pdb=" OD1 ASP C 127 " model vdw 2.092 2.520 nonbonded pdb=" O ASP F 439 " pdb=" OG1 THR F 442 " model vdw 2.163 2.440 nonbonded pdb=" O ARG A 820 " pdb=" OG SER A 823 " model vdw 2.176 2.440 nonbonded pdb=" OD1 ASP B 258 " pdb=" OG SER B 287 " model vdw 2.177 2.440 ... (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 ========== 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.740 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 55.310 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.530 ------------------------------------------------------------------------------- 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= 0.397 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 : 9.36 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (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 TRP 0.016 0.002 TRP A 316 HIS 0.005 0.001 HIS A 414 PHE 0.029 0.002 PHE A 694 TYR 0.016 0.002 TYR B 280 ARG 0.005 0.001 ARG F 239 *********************** 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 fitting. rotamer outliers: 174 poor density : 144 time to evaluate : 2.466 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: 0.8815 (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: 0.7557 (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: 0.2860 time to fit residues: 143.8167 Evaluate side-chains 208 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 119 time to evaluate : 2.280 ------------------------------------------------------------------------------- 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: 286 random chunks: chunk 241 optimal weight: 0.2980 chunk 216 optimal weight: 4.9990 chunk 120 optimal weight: 0.0770 chunk 74 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 259 optimal weight: 4.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 211 HIS A 262 ASN ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 ASN A1032 GLN A1033 ASN A1150 HIS B 221 ASN B 350 ASN B 385 GLN B 388 GLN C 79 GLN D 25 ASN D 114 HIS E 29 GLN E 223 HIS E 281 ASN F 122 GLN F 123 GLN ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20956 Z= 0.207 Angle : 0.556 7.031 28646 Z= 0.296 Chirality : 0.040 0.156 3468 Planarity : 0.004 0.050 3656 Dihedral : 7.989 77.931 3205 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.12 % Favored : 94.85 % Rotamer: Outliers : 5.71 % Allowed : 23.57 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 2837 helix: 1.03 (0.13), residues: 1653 sheet: -0.70 (0.33), residues: 242 loop : -2.39 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1018 HIS 0.003 0.001 HIS E 223 PHE 0.020 0.001 PHE A 694 TYR 0.013 0.001 TYR B 280 ARG 0.002 0.000 ARG B 313 *********************** 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 236 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 134 time to evaluate : 2.474 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.8942 (tpp) cc_final: 0.8519 (tpp) REVERT: A 791 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8665 (mt) REVERT: A 893 ASN cc_start: 0.9233 (OUTLIER) cc_final: 0.8952 (t0) REVERT: A 1094 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.6638 (t80) REVERT: A 1148 MET cc_start: 0.9209 (mmm) cc_final: 0.8633 (mmp) REVERT: B 150 TRP cc_start: 0.8913 (m-10) cc_final: 0.8078 (m-10) REVERT: B 258 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7993 (t0) REVERT: B 278 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9146 (tt) REVERT: B 318 GLU cc_start: 0.8295 (tp30) cc_final: 0.8027 (tp30) REVERT: B 367 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8720 (tt) REVERT: B 435 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8270 (mm) REVERT: B 449 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8238 (mt) REVERT: C 107 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.7371 (t80) REVERT: C 146 LYS cc_start: 0.9249 (mmtt) cc_final: 0.9017 (mmtp) REVERT: C 176 ASN cc_start: 0.8552 (m-40) cc_final: 0.8110 (t0) REVERT: C 188 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.7049 (t80) REVERT: D 29 ASP cc_start: 0.9390 (t0) cc_final: 0.9044 (t0) REVERT: D 132 GLN cc_start: 0.8396 (tp40) cc_final: 0.7480 (tm-30) REVERT: E 318 MET cc_start: 0.7735 (ttm) cc_final: 0.7273 (ttm) REVERT: F 244 MET cc_start: -0.0627 (mpp) cc_final: -0.0942 (mpp) outliers start: 102 outliers final: 54 residues processed: 230 average time/residue: 0.2763 time to fit residues: 105.1441 Evaluate side-chains 185 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 121 time to evaluate : 2.349 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 441 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 569 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 744 ASN 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 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 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 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 185 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 435 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 536 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 107 PHE 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 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 334 ILE 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: 286 random chunks: chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 216 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 281 optimal weight: 30.0000 chunk 231 optimal weight: 4.9990 chunk 258 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 529 HIS ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN E 252 HIS F 90 GLN ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20956 Z= 0.307 Angle : 0.586 8.824 28646 Z= 0.311 Chirality : 0.042 0.161 3468 Planarity : 0.004 0.045 3656 Dihedral : 7.005 59.989 3128 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.71 % Rotamer: Outliers : 6.77 % Allowed : 22.79 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2837 helix: 1.43 (0.13), residues: 1667 sheet: -0.45 (0.33), residues: 239 loop : -2.16 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1018 HIS 0.004 0.001 HIS A 136 PHE 0.025 0.002 PHE A 694 TYR 0.013 0.001 TYR A 839 ARG 0.004 0.000 ARG C 76 *********************** 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 247 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 126 time to evaluate : 2.425 Fit side-chains revert: symmetry clash REVERT: A 110 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8908 (t80) REVERT: A 744 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8075 (m-40) REVERT: A 791 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8679 (mt) REVERT: A 1094 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.6854 (t80) REVERT: A 1148 MET cc_start: 0.9135 (mmm) cc_final: 0.8637 (mmp) REVERT: B 98 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.9008 (mt) REVERT: B 214 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7773 (mt) REVERT: B 258 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7967 (t0) REVERT: B 367 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.8916 (tt) REVERT: B 376 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9094 (mt) REVERT: B 449 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8273 (mt) REVERT: C 107 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.7123 (t80) REVERT: C 188 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.7025 (t80) REVERT: D 29 ASP cc_start: 0.9457 (t0) cc_final: 0.9073 (t0) REVERT: D 132 GLN cc_start: 0.8347 (tp40) cc_final: 0.7353 (tm-30) REVERT: E 82 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6453 (mmm160) REVERT: E 318 MET cc_start: 0.7754 (ttm) cc_final: 0.7300 (ttm) REVERT: F 392 HIS cc_start: 0.8456 (m170) cc_final: 0.8191 (m170) outliers start: 121 outliers final: 72 residues processed: 236 average time/residue: 0.2888 time to fit residues: 111.3827 Evaluate side-chains 204 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 119 time to evaluate : 2.198 ------------------------------------------------------------------------------- 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 413 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 457 THR 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 664 THR Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 744 ASN 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 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 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 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 75 ASP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 185 LEU 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 367 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 435 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 536 THR 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 107 PHE 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 82 ARG 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 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 329 SER 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: 286 random chunks: chunk 257 optimal weight: 50.0000 chunk 195 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 276 optimal weight: 10.0000 chunk 136 optimal weight: 0.9990 chunk 247 optimal weight: 0.0980 chunk 74 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 GLN ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20956 Z= 0.163 Angle : 0.513 8.604 28646 Z= 0.269 Chirality : 0.039 0.145 3468 Planarity : 0.003 0.044 3656 Dihedral : 6.289 59.080 3116 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 4.65 % Allowed : 25.64 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.17), residues: 2837 helix: 1.87 (0.13), residues: 1668 sheet: -0.21 (0.34), residues: 242 loop : -1.95 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1018 HIS 0.005 0.001 HIS A 136 PHE 0.017 0.001 PHE A 694 TYR 0.028 0.001 TYR F 349 ARG 0.007 0.000 ARG F 295 *********************** 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 216 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 133 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 MET cc_start: 0.8798 (tpp) cc_final: 0.8581 (tpt) REVERT: A 744 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7638 (m-40) REVERT: A 791 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8640 (mt) REVERT: A 1094 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.6780 (t80) REVERT: B 150 TRP cc_start: 0.8957 (m-10) cc_final: 0.8070 (m-10) REVERT: B 258 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8092 (t0) REVERT: B 278 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9116 (tt) REVERT: B 367 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8954 (tt) REVERT: B 376 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9043 (mt) REVERT: C 107 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.7102 (t80) REVERT: C 188 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.7047 (t80) REVERT: D 29 ASP cc_start: 0.9379 (t0) cc_final: 0.8975 (t0) REVERT: D 132 GLN cc_start: 0.8245 (tp40) cc_final: 0.7329 (tm-30) REVERT: E 318 MET cc_start: 0.7740 (ttm) cc_final: 0.7289 (ttm) REVERT: E 373 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8299 (tp) REVERT: F 156 TYR cc_start: -0.0049 (m-80) cc_final: -0.0277 (m-80) REVERT: F 392 HIS cc_start: 0.8474 (m170) cc_final: 0.8184 (m170) outliers start: 83 outliers final: 47 residues processed: 209 average time/residue: 0.2953 time to fit residues: 102.2717 Evaluate side-chains 185 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 128 time to evaluate : 2.432 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 441 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 500 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 744 ASN 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 852 TYR Chi-restraints excluded: chain A residue 864 THR 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 1041 PHE Chi-restraints excluded: chain A residue 1094 PHE 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 258 ASP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 107 PHE 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 202 LEU Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 140 LEU 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 373 LEU Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 360 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 230 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 205 optimal weight: 4.9990 chunk 114 optimal weight: 30.0000 chunk 235 optimal weight: 5.9990 chunk 191 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 893 ASN E 72 HIS F 123 GLN ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2104 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= 0.368 Angle : 0.606 8.490 28646 Z= 0.320 Chirality : 0.042 0.155 3468 Planarity : 0.004 0.044 3656 Dihedral : 6.322 59.146 3109 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.68 % Favored : 94.28 % Rotamer: Outliers : 5.49 % Allowed : 25.42 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.17), residues: 2837 helix: 1.87 (0.13), residues: 1660 sheet: -0.01 (0.35), residues: 236 loop : -1.99 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 316 HIS 0.004 0.001 HIS A 136 PHE 0.026 0.002 PHE A 694 TYR 0.013 0.002 TYR A 963 ARG 0.005 0.000 ARG A 858 *********************** 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 222 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 124 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 587 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8815 (tt) REVERT: A 744 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.7904 (m-40) REVERT: A 791 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8655 (mt) REVERT: A 1094 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.6784 (t80) REVERT: B 214 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7767 (mt) REVERT: B 258 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8054 (t0) REVERT: B 357 GLN cc_start: 0.8585 (tp40) cc_final: 0.8326 (tp40) REVERT: B 367 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8985 (tt) REVERT: B 376 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8964 (mt) REVERT: C 107 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.6948 (t80) REVERT: C 188 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.7005 (t80) REVERT: D 29 ASP cc_start: 0.9468 (t0) cc_final: 0.9096 (t0) REVERT: D 132 GLN cc_start: 0.8432 (tp40) cc_final: 0.7347 (tm-30) REVERT: E 318 MET cc_start: 0.7834 (ttm) cc_final: 0.7378 (ttm) REVERT: E 373 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8270 (tp) REVERT: F 156 TYR cc_start: -0.0023 (m-80) cc_final: -0.0302 (m-80) REVERT: F 244 MET cc_start: 0.1151 (mpp) cc_final: -0.0405 (mmm) REVERT: F 392 HIS cc_start: 0.8590 (m170) cc_final: 0.8322 (m-70) outliers start: 98 outliers final: 71 residues processed: 215 average time/residue: 0.2793 time to fit residues: 99.8621 Evaluate side-chains 203 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 121 time to evaluate : 2.152 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 441 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 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 587 LEU Chi-restraints excluded: chain A residue 664 THR 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 744 ASN 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 864 THR 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 1007 THR 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 15 LEU Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 196 THR 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 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 376 LEU 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 493 PHE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 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 105 ILE Chi-restraints excluded: chain E residue 140 LEU 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 373 LEU Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 329 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 93 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 276 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 91 optimal weight: 20.0000 chunk 145 optimal weight: 6.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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** F 123 GLN ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20956 Z= 0.193 Angle : 0.529 10.283 28646 Z= 0.277 Chirality : 0.040 0.145 3468 Planarity : 0.003 0.047 3656 Dihedral : 5.882 59.052 3104 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.38 % Rotamer: Outliers : 4.59 % Allowed : 26.65 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2837 helix: 2.11 (0.13), residues: 1658 sheet: 0.14 (0.35), residues: 241 loop : -1.84 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1018 HIS 0.002 0.001 HIS A 875 PHE 0.018 0.001 PHE A 694 TYR 0.025 0.001 TYR F 349 ARG 0.003 0.000 ARG A 858 *********************** 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 208 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 126 time to evaluate : 2.409 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7542 (tm-30) REVERT: A 298 MET cc_start: 0.8881 (tpp) cc_final: 0.8608 (tpt) REVERT: A 744 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.7935 (m-40) REVERT: A 791 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8611 (mt) REVERT: A 828 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8654 (pm20) REVERT: A 861 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7587 (tp30) REVERT: A 1094 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.6810 (t80) REVERT: A 1148 MET cc_start: 0.8994 (mmm) cc_final: 0.8351 (mmp) REVERT: B 150 TRP cc_start: 0.8990 (m-10) cc_final: 0.8119 (m-10) REVERT: B 258 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8089 (t0) REVERT: B 357 GLN cc_start: 0.8590 (tp40) cc_final: 0.8318 (tp40) REVERT: B 367 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8924 (tt) REVERT: B 376 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9040 (mt) REVERT: C 107 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.6897 (t80) REVERT: C 188 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6927 (t80) REVERT: D 29 ASP cc_start: 0.9397 (t0) cc_final: 0.9005 (t0) REVERT: D 132 GLN cc_start: 0.8335 (tp40) cc_final: 0.7335 (tm-30) REVERT: E 318 MET cc_start: 0.7815 (ttm) cc_final: 0.7348 (ttm) REVERT: E 373 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8210 (tp) REVERT: F 156 TYR cc_start: -0.0067 (m-80) cc_final: -0.0324 (m-80) REVERT: F 392 HIS cc_start: 0.8603 (m170) cc_final: 0.8323 (m-70) outliers start: 82 outliers final: 58 residues processed: 200 average time/residue: 0.2905 time to fit residues: 97.4713 Evaluate side-chains 191 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 122 time to evaluate : 2.397 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 441 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 500 LEU 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 744 ASN 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 828 GLN 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 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 127 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 258 ASP 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 376 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 33 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 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 105 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 201 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 310 LEU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 329 SER 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: 286 random chunks: chunk 266 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 157 optimal weight: 0.0670 chunk 202 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 232 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 275 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.5924 ------------------------------------------------------------------------------- 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** ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2417 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= 0.257 Angle : 0.554 10.530 28646 Z= 0.290 Chirality : 0.040 0.143 3468 Planarity : 0.003 0.042 3656 Dihedral : 5.810 59.604 3102 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.19 % Favored : 94.78 % Rotamer: Outliers : 4.98 % Allowed : 26.37 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.17), residues: 2837 helix: 2.12 (0.13), residues: 1661 sheet: 0.15 (0.35), residues: 242 loop : -1.85 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1018 HIS 0.003 0.001 HIS A 136 PHE 0.022 0.001 PHE A 694 TYR 0.046 0.001 TYR F 349 ARG 0.003 0.000 ARG A 858 *********************** 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 212 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 123 time to evaluate : 2.456 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7595 (tm-30) REVERT: A 139 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8931 (mt) REVERT: A 319 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8489 (t) REVERT: A 744 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8017 (m-40) REVERT: A 791 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8648 (mt) REVERT: A 861 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7705 (tp30) REVERT: A 1094 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.6697 (t80) REVERT: B 258 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8238 (t0) REVERT: B 357 GLN cc_start: 0.8610 (tp40) cc_final: 0.8330 (tp40) REVERT: B 367 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8888 (tt) REVERT: B 376 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9114 (mt) REVERT: C 107 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.6915 (t80) REVERT: C 188 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.7051 (t80) REVERT: D 29 ASP cc_start: 0.9397 (t0) cc_final: 0.9065 (t0) REVERT: E 318 MET cc_start: 0.7829 (ttm) cc_final: 0.7357 (ttm) REVERT: E 373 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8156 (tp) outliers start: 89 outliers final: 68 residues processed: 202 average time/residue: 0.2797 time to fit residues: 93.7969 Evaluate side-chains 203 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 123 time to evaluate : 2.317 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 319 VAL 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 457 THR 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 615 ASN Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 744 ASN 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 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 1007 THR Chi-restraints excluded: chain A residue 1078 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 127 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 258 ASP 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 376 LEU Chi-restraints excluded: chain B residue 466 ILE 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 C residue 30 ILE Chi-restraints excluded: chain C residue 33 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 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 77 SER 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 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 E residue 373 LEU Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 329 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 170 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 chunk 164 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 175 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 216 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20956 Z= 0.192 Angle : 0.528 10.857 28646 Z= 0.274 Chirality : 0.039 0.142 3468 Planarity : 0.003 0.043 3656 Dihedral : 5.574 59.959 3102 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 4.70 % Allowed : 26.76 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.17), residues: 2837 helix: 2.18 (0.13), residues: 1679 sheet: 0.29 (0.35), residues: 240 loop : -1.81 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1018 HIS 0.002 0.001 HIS A 875 PHE 0.019 0.001 PHE A 694 TYR 0.047 0.001 TYR F 349 ARG 0.003 0.000 ARG A 858 *********************** 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 209 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 125 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.9008 (mt) cc_final: 0.8655 (mt) REVERT: A 138 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7531 (tm-30) REVERT: A 298 MET cc_start: 0.8995 (tpp) cc_final: 0.8738 (tpp) REVERT: A 744 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8031 (m-40) REVERT: A 791 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8665 (mt) REVERT: A 828 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8669 (pm20) REVERT: A 861 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7578 (tp30) REVERT: A 1094 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.6784 (t80) REVERT: B 258 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8251 (t0) REVERT: B 357 GLN cc_start: 0.8654 (tp40) cc_final: 0.8377 (tp40) REVERT: B 367 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8905 (tt) REVERT: B 376 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9017 (mt) REVERT: C 107 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.6917 (t80) REVERT: C 188 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.7096 (t80) REVERT: D 29 ASP cc_start: 0.9393 (t0) cc_final: 0.9099 (t0) REVERT: D 132 GLN cc_start: 0.8465 (tp40) cc_final: 0.7480 (tm-30) REVERT: E 318 MET cc_start: 0.7827 (ttm) cc_final: 0.7343 (ttm) REVERT: E 373 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8122 (tp) REVERT: F 392 HIS cc_start: 0.8486 (m170) cc_final: 0.8268 (m-70) REVERT: F 423 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7579 (mt0) outliers start: 84 outliers final: 65 residues processed: 201 average time/residue: 0.2946 time to fit residues: 96.7947 Evaluate side-chains 197 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 120 time to evaluate : 2.306 ------------------------------------------------------------------------------- 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 154 GLN 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 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 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 676 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 744 ASN 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 828 GLN Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 864 THR 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 1007 THR 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 127 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 258 ASP 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 376 LEU Chi-restraints excluded: chain B residue 443 VAL 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 C residue 30 ILE Chi-restraints excluded: chain C residue 33 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 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 202 LEU 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 248 LYS Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 329 SER 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 423 GLN Chi-restraints excluded: chain F residue 430 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 250 optimal weight: 0.0170 chunk 264 optimal weight: 20.0000 chunk 240 optimal weight: 1.9990 chunk 256 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 201 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 232 optimal weight: 9.9990 chunk 242 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- 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** E 29 GLN F 186 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20956 Z= 0.226 Angle : 0.546 11.739 28646 Z= 0.283 Chirality : 0.040 0.140 3468 Planarity : 0.003 0.037 3656 Dihedral : 5.493 59.324 3097 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.74 % Rotamer: Outliers : 4.76 % Allowed : 26.82 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.17), residues: 2837 helix: 2.24 (0.13), residues: 1665 sheet: 0.12 (0.36), residues: 230 loop : -1.70 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 532 HIS 0.003 0.001 HIS A 136 PHE 0.021 0.001 PHE A 694 TYR 0.050 0.001 TYR F 349 ARG 0.003 0.000 ARG C 76 *********************** 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 210 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 125 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 744 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7942 (m-40) REVERT: A 787 MET cc_start: 0.8167 (mmm) cc_final: 0.7874 (mmm) REVERT: A 828 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8662 (pm20) REVERT: A 861 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7653 (tp30) REVERT: A 1094 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.6609 (t80) REVERT: B 258 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8261 (t0) REVERT: B 357 GLN cc_start: 0.8684 (tp40) cc_final: 0.8407 (tp40) REVERT: B 367 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8893 (tt) REVERT: C 107 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.6932 (t80) REVERT: C 188 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.7217 (t80) REVERT: D 29 ASP cc_start: 0.9391 (t0) cc_final: 0.9107 (t0) REVERT: E 373 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8129 (tp) REVERT: F 392 HIS cc_start: 0.8290 (m170) cc_final: 0.8067 (m-70) outliers start: 85 outliers final: 69 residues processed: 200 average time/residue: 0.2731 time to fit residues: 90.5011 Evaluate side-chains 199 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 121 time to evaluate : 2.328 ------------------------------------------------------------------------------- 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 154 GLN 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 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 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 676 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 744 ASN 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 828 GLN Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 864 THR 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 1007 THR 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 126 THR Chi-restraints excluded: chain B residue 127 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 258 ASP Chi-restraints excluded: chain B residue 268 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 443 VAL Chi-restraints excluded: chain B residue 466 ILE 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 C residue 30 ILE Chi-restraints excluded: chain C residue 33 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 147 TRP Chi-restraints excluded: chain C residue 158 GLU 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 105 ILE Chi-restraints excluded: chain E residue 201 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 310 LEU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 329 SER 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: 286 random chunks: chunk 168 optimal weight: 6.9990 chunk 271 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 284 optimal weight: 9.9990 chunk 262 optimal weight: 30.0000 chunk 226 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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** ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 20956 Z= 0.495 Angle : 0.694 11.727 28646 Z= 0.363 Chirality : 0.044 0.177 3468 Planarity : 0.004 0.038 3656 Dihedral : 5.865 58.911 3095 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.82 % Allowed : 26.82 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.17), residues: 2837 helix: 1.85 (0.13), residues: 1669 sheet: 0.10 (0.35), residues: 238 loop : -1.92 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 580 HIS 0.005 0.001 HIS A1150 PHE 0.029 0.002 PHE A 694 TYR 0.051 0.002 TYR F 349 ARG 0.006 0.001 ARG A 714 ********************** 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 207 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 121 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 MET cc_start: 0.9068 (tpp) cc_final: 0.8792 (tpp) REVERT: A 744 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8048 (m-40) REVERT: A 1094 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.6901 (t80) REVERT: A 1148 MET cc_start: 0.9080 (mmm) cc_final: 0.8388 (mmp) REVERT: B 258 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8285 (t0) REVERT: B 357 GLN cc_start: 0.8658 (tp40) cc_final: 0.8377 (tp40) REVERT: B 367 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8882 (tt) REVERT: B 376 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9048 (mt) REVERT: C 107 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.6986 (t80) REVERT: C 180 GLN cc_start: 0.8516 (tt0) cc_final: 0.8058 (tm-30) REVERT: D 29 ASP cc_start: 0.9482 (t0) cc_final: 0.9171 (t0) REVERT: E 318 MET cc_start: 0.8726 (mmm) cc_final: 0.8473 (tpp) REVERT: E 373 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8170 (tp) REVERT: F 392 HIS cc_start: 0.8296 (m170) cc_final: 0.8068 (m-70) outliers start: 86 outliers final: 71 residues processed: 200 average time/residue: 0.2733 time to fit residues: 90.8662 Evaluate side-chains 197 residues out of total 2646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 119 time to evaluate : 2.335 ------------------------------------------------------------------------------- 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 154 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 SER 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 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 676 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 744 ASN 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 864 THR 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 1007 THR 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 126 THR Chi-restraints excluded: chain B residue 127 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 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 367 LEU Chi-restraints excluded: chain B residue 376 LEU 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 493 PHE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 536 THR 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 202 LEU Chi-restraints excluded: chain E residue 77 SER 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 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 E residue 373 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 335 THR 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: 286 random chunks: chunk 180 optimal weight: 5.9990 chunk 241 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 209 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 233 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.104307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.065216 restraints weight = 99194.099| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 4.55 r_work: 0.2828 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2878 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= 0.172 Angle : 0.538 11.886 28646 Z= 0.278 Chirality : 0.039 0.161 3468 Planarity : 0.003 0.038 3656 Dihedral : 5.408 59.966 3093 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.42 % Allowed : 28.39 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.17), residues: 2837 helix: 2.25 (0.13), residues: 1664 sheet: 0.20 (0.35), residues: 240 loop : -1.77 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1018 HIS 0.002 0.001 HIS A 875 PHE 0.016 0.001 PHE A 694 TYR 0.053 0.001 TYR F 349 ARG 0.003 0.000 ARG F 295 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4236.70 seconds wall clock time: 77 minutes 23.74 seconds (4643.74 seconds total)