Starting phenix.real_space_refine on Fri Aug 22 22:31:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ket_37167/08_2025/8ket_37167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ket_37167/08_2025/8ket_37167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ket_37167/08_2025/8ket_37167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ket_37167/08_2025/8ket_37167.map" model { file = "/net/cci-nas-00/data/ceres_data/8ket_37167/08_2025/8ket_37167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ket_37167/08_2025/8ket_37167.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 25 5.16 5 C 5200 2.51 5 N 1531 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8399 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1323 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 233} Link IDs: {'PTRANS': 7, 'TRANS': 258} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 918 Unresolved non-hydrogen angles: 1184 Unresolved non-hydrogen dihedrals: 798 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'PHE:plan': 27, 'ARG:plan': 12, 'HIS:plan': 9, 'TYR:plan': 13, 'GLN:plan1': 6, 'GLU:plan': 9, 'TRP:plan': 4, 'ASP:plan': 8, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 487 Chain: "B" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1436 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PTRANS': 7, 'TRANS': 259} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 805 Unresolved non-hydrogen angles: 1034 Unresolved non-hydrogen dihedrals: 697 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'PHE:plan': 25, 'ARG:plan': 13, 'GLN:plan1': 4, 'GLU:plan': 9, 'HIS:plan': 7, 'TRP:plan': 4, 'TYR:plan': 8, 'ASP:plan': 8, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 427 Chain: "F" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1801 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 21, 'TRANS': 234} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 18, 'PHE:plan': 5, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'ARG:plan': 4, 'GLN:plan1': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 175 Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "C" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 3682 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PTRANS': 9, 'TRANS': 527} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 578 Unresolved non-hydrogen angles: 734 Unresolved non-hydrogen dihedrals: 498 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 20, 'GLU:plan': 7, 'TYR:plan': 14, 'ASN:plan1': 11, 'PHE:plan': 7, 'ASP:plan': 7, 'HIS:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 366 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 2, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.91, per 1000 atoms: 0.23 Number of scatterers: 8399 At special positions: 0 Unit cell: (98.44, 105.93, 148.73, 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 25 16.00 O 1643 8.00 N 1531 7.00 C 5200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS F 79 " - pdb=" SG CYS F 261 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 199 " - pdb=" SG CYS F 232 " distance=2.03 Simple disulfide: pdb=" SG CYS C 311 " - pdb=" SG CYS C 539 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " ALPHA1-6 " MAN D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 6 " BETA1-3 " NAG D 1 " - " NAG D 2 " " MAN D 4 " - " BMA D 5 " BETA1-4 " MAN D 3 " - " BMA D 7 " NAG-ASN " NAG C 801 " - " ASN C 217 " " NAG C 802 " - " ASN C 272 " " NAG C 803 " - " ASN C 431 " " NAG C 804 " - " ASN C 608 " " NAG D 1 " - " ASN H 350 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 288.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2496 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 5 sheets defined 72.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 1 through 26 removed outlier: 4.209A pdb=" N LEU A 25 " --> pdb=" O HIS A 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 39 through 66 Processing helix chain 'A' and resid 72 through 96 removed outlier: 3.672A pdb=" N THR A 86 " --> pdb=" O TRP A 82 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 130 removed outlier: 4.007A pdb=" N VAL A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 166 Processing helix chain 'A' and resid 169 through 200 removed outlier: 4.230A pdb=" N VAL A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 237 removed outlier: 4.403A pdb=" N ALA A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 266 removed outlier: 3.564A pdb=" N TYR A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 26 removed outlier: 3.512A pdb=" N MET B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 25 " --> pdb=" O HIS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 39 through 66 removed outlier: 3.712A pdb=" N VAL B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 56 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 65 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 95 removed outlier: 3.671A pdb=" N TYR B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 93 " --> pdb=" O CYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 130 removed outlier: 3.550A pdb=" N ALA B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 166 Processing helix chain 'B' and resid 169 through 201 removed outlier: 4.294A pdb=" N VAL B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 236 removed outlier: 4.444A pdb=" N VAL B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 267 Processing helix chain 'F' and resid 99 through 111 removed outlier: 3.913A pdb=" N LEU F 103 " --> pdb=" O ASN F 99 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 104 " --> pdb=" O PRO F 100 " (cutoff:3.500A) Proline residue: F 106 - end of helix removed outlier: 3.799A pdb=" N SER F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 169 removed outlier: 3.604A pdb=" N LEU F 160 " --> pdb=" O ALA F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 removed outlier: 4.401A pdb=" N SER F 245 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 286 removed outlier: 3.636A pdb=" N VAL F 286 " --> pdb=" O GLU F 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 197 removed outlier: 3.620A pdb=" N ILE C 193 " --> pdb=" O THR C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 216 removed outlier: 3.701A pdb=" N TYR C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS C 212 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 232 removed outlier: 3.810A pdb=" N ARG C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 253 removed outlier: 3.587A pdb=" N GLU C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU C 252 " --> pdb=" O LYS C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 268 removed outlier: 3.810A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.638A pdb=" N VAL C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 304 removed outlier: 3.582A pdb=" N TRP C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 329 removed outlier: 3.653A pdb=" N HIS C 317 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 321 " --> pdb=" O HIS C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 348 Processing helix chain 'C' and resid 362 through 370 Processing helix chain 'C' and resid 372 through 385 Processing helix chain 'C' and resid 393 through 408 removed outlier: 3.656A pdb=" N ALA C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 423 Processing helix chain 'C' and resid 430 through 445 removed outlier: 3.828A pdb=" N ALA C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET C 444 " --> pdb=" O LYS C 440 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 460 Processing helix chain 'C' and resid 466 through 481 removed outlier: 3.740A pdb=" N LYS C 476 " --> pdb=" O LYS C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 495 removed outlier: 3.516A pdb=" N LEU C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET C 492 " --> pdb=" O GLN C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 516 removed outlier: 3.768A pdb=" N GLN C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 532 removed outlier: 3.524A pdb=" N SER C 531 " --> pdb=" O GLN C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 551 removed outlier: 3.796A pdb=" N ALA C 542 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN C 548 " --> pdb=" O GLU C 544 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 549 " --> pdb=" O LEU C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 Processing helix chain 'C' and resid 571 through 585 removed outlier: 3.536A pdb=" N VAL C 575 " --> pdb=" O TYR C 571 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 3.912A pdb=" N ALA C 594 " --> pdb=" O GLN C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 623 removed outlier: 3.813A pdb=" N HIS C 617 " --> pdb=" O ARG C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 640 removed outlier: 3.549A pdb=" N HIS C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 660 removed outlier: 3.538A pdb=" N SER C 658 " --> pdb=" O TYR C 654 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN C 660 " --> pdb=" O LEU C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 677 removed outlier: 3.582A pdb=" N MET C 667 " --> pdb=" O SER C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 698 removed outlier: 3.863A pdb=" N ALA C 694 " --> pdb=" O PHE C 690 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 695 " --> pdb=" O TYR C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 723 removed outlier: 3.594A pdb=" N ALA C 708 " --> pdb=" O PRO C 704 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 43 through 46 removed outlier: 6.149A pdb=" N ARG F 44 " --> pdb=" O ILE F 259 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N CYS F 261 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN F 46 " --> pdb=" O CYS F 261 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N SER F 263 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ASP F 258 " --> pdb=" O PRO F 82 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE F 260 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASN F 65 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 10.543A pdb=" N LEU F 83 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N GLU F 63 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 122 through 125 removed outlier: 6.057A pdb=" N ILE F 131 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR F 149 " --> pdb=" O GLN F 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 178 through 181 Processing sheet with id=AA4, first strand: chain 'F' and resid 189 through 193 removed outlier: 7.310A pdb=" N SER F 208 " --> pdb=" O TYR F 234 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N VAL F 236 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR F 210 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE F 238 " --> pdb=" O THR F 210 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET F 212 " --> pdb=" O ILE F 238 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR F 240 " --> pdb=" O MET F 212 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE F 214 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLU F 233 " --> pdb=" O GLU F 228 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU F 228 " --> pdb=" O GLU F 233 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLU F 235 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL F 226 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL F 237 " --> pdb=" O LEU F 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 198 through 199 removed outlier: 3.732A pdb=" N ARG F 205 " --> pdb=" O CYS F 199 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 2091 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: 1.23 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2333 1.34 - 1.46: 1558 1.46 - 1.58: 4583 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 8512 Sorted by residual: bond pdb=" CA ARG C 689 " pdb=" C ARG C 689 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.27e-02 6.20e+03 1.13e+01 bond pdb=" C6 MAN D 4 " pdb=" O6 MAN D 4 " ideal model delta sigma weight residual 1.407 1.466 -0.059 2.00e-02 2.50e+03 8.58e+00 bond pdb=" CB CYS C 539 " pdb=" SG CYS C 539 " ideal model delta sigma weight residual 1.808 1.723 0.085 3.30e-02 9.18e+02 6.68e+00 bond pdb=" CA LYS C 688 " pdb=" C LYS C 688 " ideal model delta sigma weight residual 1.524 1.494 0.030 1.29e-02 6.01e+03 5.31e+00 bond pdb=" C1 NAG C 803 " pdb=" O5 NAG C 803 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.69e+00 ... (remaining 8507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 11280 1.85 - 3.69: 339 3.69 - 5.54: 50 5.54 - 7.39: 11 7.39 - 9.24: 5 Bond angle restraints: 11685 Sorted by residual: angle pdb=" CA TYR B 23 " pdb=" CB TYR B 23 " pdb=" CG TYR B 23 " ideal model delta sigma weight residual 113.90 120.42 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" CB LYS F 74 " pdb=" CG LYS F 74 " pdb=" CD LYS F 74 " ideal model delta sigma weight residual 111.30 119.37 -8.07 2.30e+00 1.89e-01 1.23e+01 angle pdb=" C GLN F 203 " pdb=" N ASN F 204 " pdb=" CA ASN F 204 " ideal model delta sigma weight residual 122.46 127.17 -4.71 1.41e+00 5.03e-01 1.12e+01 angle pdb=" CB GLN C 240 " pdb=" CG GLN C 240 " pdb=" CD GLN C 240 " ideal model delta sigma weight residual 112.60 117.87 -5.27 1.70e+00 3.46e-01 9.61e+00 angle pdb=" N GLU C 432 " pdb=" CA GLU C 432 " pdb=" C GLU C 432 " ideal model delta sigma weight residual 111.07 114.18 -3.11 1.07e+00 8.73e-01 8.43e+00 ... (remaining 11680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.69: 4783 25.69 - 51.38: 274 51.38 - 77.07: 39 77.07 - 102.76: 31 102.76 - 128.45: 21 Dihedral angle restraints: 5148 sinusoidal: 1284 harmonic: 3864 Sorted by residual: dihedral pdb=" CA CYS C 539 " pdb=" C CYS C 539 " pdb=" N HIS C 540 " pdb=" CA HIS C 540 " ideal model delta harmonic sigma weight residual -180.00 -153.89 -26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA CYS C 311 " pdb=" C CYS C 311 " pdb=" N GLU C 312 " pdb=" CA GLU C 312 " ideal model delta harmonic sigma weight residual 180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA SER F 38 " pdb=" C SER F 38 " pdb=" N ASP F 39 " pdb=" CA ASP F 39 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 5145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.257: 1446 0.257 - 0.515: 0 0.515 - 0.772: 1 0.772 - 1.029: 0 1.029 - 1.286: 1 Chirality restraints: 1448 Sorted by residual: chirality pdb=" C1 MAN D 3 " pdb=" O4 NAG D 2 " pdb=" C2 MAN D 3 " pdb=" O5 MAN D 3 " both_signs ideal model delta sigma weight residual False 2.40 1.87 0.53 2.00e-02 2.50e+03 7.01e+02 chirality pdb=" C1 MAN D 6 " pdb=" O6 MAN D 4 " pdb=" C2 MAN D 6 " pdb=" O5 MAN D 6 " both_signs ideal model delta sigma weight residual False 2.40 2.65 -0.25 2.00e-02 2.50e+03 1.53e+02 chirality pdb=" C1 BMA D 7 " pdb=" O4 MAN D 3 " pdb=" C2 BMA D 7 " pdb=" O5 BMA D 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.23e+01 ... (remaining 1445 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.342 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG D 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.103 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.297 2.00e-02 2.50e+03 2.50e-01 7.80e+02 pdb=" C7 NAG D 1 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.427 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 608 " 0.032 2.00e-02 2.50e+03 3.07e-02 1.18e+01 pdb=" CG ASN C 608 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN C 608 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 608 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG C 804 " 0.034 2.00e-02 2.50e+03 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1822 2.77 - 3.30: 7904 3.30 - 3.84: 13859 3.84 - 4.37: 14220 4.37 - 4.90: 25501 Nonbonded interactions: 63306 Sorted by model distance: nonbonded pdb=" O SER C 273 " pdb=" OG SER C 273 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP C 635 " pdb=" OH TYR C 654 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP C 598 " pdb=" OH TYR C 636 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR F 122 " pdb=" O TYR F 134 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR F 61 " pdb=" O ASP F 258 " model vdw 2.300 3.040 ... (remaining 63301 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (name N or name CA or name C or name O or name CB )) selection = (chain 'B' and ((resid 1 through 57 and (name N or name CA or name C or name O o \ r name CB )) or resid 58 through 266)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.120 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 8527 Z= 0.209 Angle : 0.793 11.972 11726 Z= 0.414 Chirality : 0.057 1.286 1448 Planarity : 0.011 0.297 1568 Dihedral : 21.356 128.454 2640 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.13 % Rotamer: Outliers : 1.70 % Allowed : 26.75 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.20), residues: 1317 helix: -0.99 (0.14), residues: 923 sheet: -0.61 (0.60), residues: 81 loop : -1.69 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 285 TYR 0.035 0.002 TYR F 123 PHE 0.009 0.001 PHE F 260 TRP 0.011 0.002 TRP C 555 HIS 0.007 0.001 HIS C 540 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8512) covalent geometry : angle 0.73905 (11685) SS BOND : bond 0.00621 ( 4) SS BOND : angle 4.34475 ( 8) hydrogen bonds : bond 0.23284 ( 703) hydrogen bonds : angle 7.49306 ( 2091) link_ALPHA1-4 : bond 0.00807 ( 1) link_ALPHA1-4 : angle 7.55633 ( 3) link_ALPHA1-6 : bond 0.02556 ( 2) link_ALPHA1-6 : angle 5.14733 ( 6) link_BETA1-3 : bond 0.00268 ( 2) link_BETA1-3 : angle 1.63279 ( 6) link_BETA1-4 : bond 0.00615 ( 1) link_BETA1-4 : angle 1.99040 ( 3) link_NAG-ASN : bond 0.00909 ( 5) link_NAG-ASN : angle 5.70466 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 285 ARG cc_start: 0.6799 (ttp-110) cc_final: 0.6575 (ttm-80) outliers start: 8 outliers final: 6 residues processed: 138 average time/residue: 0.0733 time to fit residues: 14.1397 Evaluate side-chains 137 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 269 PHE Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 541 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.0370 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 130 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.276267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.249337 restraints weight = 9622.096| |-----------------------------------------------------------------------------| r_work (start): 0.4729 rms_B_bonded: 1.32 r_work: 0.4295 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8527 Z= 0.133 Angle : 0.626 9.938 11726 Z= 0.305 Chirality : 0.042 0.378 1448 Planarity : 0.005 0.061 1568 Dihedral : 15.580 117.357 1624 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.20 % Rotamer: Outliers : 3.82 % Allowed : 24.20 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.22), residues: 1317 helix: 0.91 (0.16), residues: 936 sheet: -0.82 (0.57), residues: 79 loop : -1.72 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 116 TYR 0.013 0.001 TYR C 234 PHE 0.008 0.001 PHE B 29 TRP 0.006 0.001 TRP C 302 HIS 0.005 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8512) covalent geometry : angle 0.59525 (11685) SS BOND : bond 0.00509 ( 4) SS BOND : angle 2.25496 ( 8) hydrogen bonds : bond 0.03880 ( 703) hydrogen bonds : angle 3.75274 ( 2091) link_ALPHA1-4 : bond 0.01004 ( 1) link_ALPHA1-4 : angle 2.83286 ( 3) link_ALPHA1-6 : bond 0.00402 ( 2) link_ALPHA1-6 : angle 1.84587 ( 6) link_BETA1-3 : bond 0.01245 ( 2) link_BETA1-3 : angle 1.82728 ( 6) link_BETA1-4 : bond 0.00090 ( 1) link_BETA1-4 : angle 3.49156 ( 3) link_NAG-ASN : bond 0.00782 ( 5) link_NAG-ASN : angle 4.54662 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 129 LYS cc_start: 0.7671 (mmtt) cc_final: 0.7315 (tppt) REVERT: F 258 ASP cc_start: 0.8461 (p0) cc_final: 0.8032 (p0) outliers start: 18 outliers final: 12 residues processed: 150 average time/residue: 0.0754 time to fit residues: 15.7115 Evaluate side-chains 141 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 539 CYS Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 683 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 24 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 60.0000 chunk 39 optimal weight: 40.0000 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 6 optimal weight: 50.0000 chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.266587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.242293 restraints weight = 9458.982| |-----------------------------------------------------------------------------| r_work (start): 0.4672 rms_B_bonded: 1.27 r_work: 0.4251 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3913 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.097 8527 Z= 0.377 Angle : 0.800 9.437 11726 Z= 0.393 Chirality : 0.049 0.342 1448 Planarity : 0.005 0.065 1568 Dihedral : 13.297 115.804 1619 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 6.58 % Allowed : 22.93 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.23), residues: 1317 helix: 1.31 (0.17), residues: 934 sheet: -1.44 (0.54), residues: 79 loop : -1.65 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 630 TYR 0.030 0.003 TYR B 23 PHE 0.023 0.002 PHE C 668 TRP 0.019 0.002 TRP C 302 HIS 0.013 0.002 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00890 ( 8512) covalent geometry : angle 0.77570 (11685) SS BOND : bond 0.00289 ( 4) SS BOND : angle 3.17378 ( 8) hydrogen bonds : bond 0.04270 ( 703) hydrogen bonds : angle 3.99963 ( 2091) link_ALPHA1-4 : bond 0.01138 ( 1) link_ALPHA1-4 : angle 2.44292 ( 3) link_ALPHA1-6 : bond 0.01132 ( 2) link_ALPHA1-6 : angle 2.85321 ( 6) link_BETA1-3 : bond 0.00867 ( 2) link_BETA1-3 : angle 1.83626 ( 6) link_BETA1-4 : bond 0.00542 ( 1) link_BETA1-4 : angle 4.58507 ( 3) link_NAG-ASN : bond 0.00626 ( 5) link_NAG-ASN : angle 3.94750 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.7852 (m-10) cc_final: 0.7641 (m-10) REVERT: F 258 ASP cc_start: 0.8374 (p0) cc_final: 0.7811 (p0) REVERT: C 235 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8603 (mp) REVERT: C 563 TYR cc_start: 0.8687 (t80) cc_final: 0.7858 (t80) outliers start: 31 outliers final: 21 residues processed: 156 average time/residue: 0.0706 time to fit residues: 15.4129 Evaluate side-chains 151 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 150 TYR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 684 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 86 optimal weight: 0.0370 chunk 62 optimal weight: 6.9990 chunk 84 optimal weight: 0.4980 chunk 66 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 39 optimal weight: 30.0000 chunk 29 optimal weight: 0.7980 chunk 108 optimal weight: 0.0040 chunk 4 optimal weight: 70.0000 overall best weight: 1.2672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 130 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.268886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.242265 restraints weight = 9476.831| |-----------------------------------------------------------------------------| r_work (start): 0.4688 rms_B_bonded: 1.49 r_work: 0.4249 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8527 Z= 0.184 Angle : 0.633 9.443 11726 Z= 0.305 Chirality : 0.043 0.318 1448 Planarity : 0.004 0.052 1568 Dihedral : 11.686 116.947 1618 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.02 % Favored : 95.90 % Rotamer: Outliers : 5.73 % Allowed : 24.42 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.23), residues: 1317 helix: 1.84 (0.17), residues: 938 sheet: -1.51 (0.56), residues: 79 loop : -1.64 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 116 TYR 0.015 0.001 TYR C 234 PHE 0.012 0.001 PHE C 668 TRP 0.010 0.002 TRP C 302 HIS 0.009 0.001 HIS F 130 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 8512) covalent geometry : angle 0.60793 (11685) SS BOND : bond 0.00303 ( 4) SS BOND : angle 2.89904 ( 8) hydrogen bonds : bond 0.03237 ( 703) hydrogen bonds : angle 3.41523 ( 2091) link_ALPHA1-4 : bond 0.01181 ( 1) link_ALPHA1-4 : angle 2.61478 ( 3) link_ALPHA1-6 : bond 0.01023 ( 2) link_ALPHA1-6 : angle 2.42062 ( 6) link_BETA1-3 : bond 0.00939 ( 2) link_BETA1-3 : angle 1.85431 ( 6) link_BETA1-4 : bond 0.01171 ( 1) link_BETA1-4 : angle 4.08025 ( 3) link_NAG-ASN : bond 0.00744 ( 5) link_NAG-ASN : angle 3.54517 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 123 TYR cc_start: 0.7389 (m-80) cc_final: 0.7118 (m-80) REVERT: F 234 TYR cc_start: 0.7811 (m-80) cc_final: 0.7372 (m-80) REVERT: F 258 ASP cc_start: 0.7990 (p0) cc_final: 0.7684 (p0) REVERT: C 235 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8442 (mp) REVERT: C 245 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6617 (mtp) REVERT: C 578 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.8407 (m-10) REVERT: C 587 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8166 (tm-30) outliers start: 27 outliers final: 14 residues processed: 148 average time/residue: 0.0639 time to fit residues: 13.3279 Evaluate side-chains 140 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain F residue 150 TYR Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 705 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 69 optimal weight: 0.2980 chunk 95 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 4 optimal weight: 60.0000 chunk 66 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 117 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.273108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.246381 restraints weight = 9594.577| |-----------------------------------------------------------------------------| r_work (start): 0.4706 rms_B_bonded: 1.55 r_work: 0.4240 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8527 Z= 0.136 Angle : 0.590 9.799 11726 Z= 0.283 Chirality : 0.041 0.300 1448 Planarity : 0.004 0.048 1568 Dihedral : 10.197 119.343 1615 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.13 % Rotamer: Outliers : 5.94 % Allowed : 24.42 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.24), residues: 1317 helix: 2.25 (0.17), residues: 938 sheet: -1.53 (0.56), residues: 79 loop : -1.56 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 116 TYR 0.014 0.001 TYR F 120 PHE 0.009 0.001 PHE C 668 TRP 0.010 0.001 TRP F 121 HIS 0.004 0.001 HIS C 674 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8512) covalent geometry : angle 0.56508 (11685) SS BOND : bond 0.00553 ( 4) SS BOND : angle 1.98676 ( 8) hydrogen bonds : bond 0.02812 ( 703) hydrogen bonds : angle 3.08949 ( 2091) link_ALPHA1-4 : bond 0.00980 ( 1) link_ALPHA1-4 : angle 2.95011 ( 3) link_ALPHA1-6 : bond 0.01382 ( 2) link_ALPHA1-6 : angle 2.42384 ( 6) link_BETA1-3 : bond 0.00920 ( 2) link_BETA1-3 : angle 1.62578 ( 6) link_BETA1-4 : bond 0.00953 ( 1) link_BETA1-4 : angle 4.47083 ( 3) link_NAG-ASN : bond 0.00488 ( 5) link_NAG-ASN : angle 3.42711 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: F 234 TYR cc_start: 0.7802 (m-80) cc_final: 0.7271 (m-80) REVERT: F 258 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7653 (p0) REVERT: C 235 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8393 (mp) REVERT: C 245 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6498 (mtp) REVERT: C 587 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8068 (tm-30) outliers start: 28 outliers final: 18 residues processed: 146 average time/residue: 0.0610 time to fit residues: 12.7253 Evaluate side-chains 145 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 539 CYS Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 705 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 98 optimal weight: 40.0000 chunk 17 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 246 HIS F 257 ASN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.270268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.247580 restraints weight = 9414.945| |-----------------------------------------------------------------------------| r_work (start): 0.4716 rms_B_bonded: 1.24 r_work: 0.4301 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8527 Z= 0.230 Angle : 0.645 10.250 11726 Z= 0.314 Chirality : 0.043 0.309 1448 Planarity : 0.004 0.049 1568 Dihedral : 9.717 120.132 1615 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 6.37 % Allowed : 25.90 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.24), residues: 1317 helix: 2.21 (0.17), residues: 936 sheet: -1.62 (0.55), residues: 79 loop : -1.51 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 132 TYR 0.017 0.002 TYR B 23 PHE 0.018 0.002 PHE C 668 TRP 0.010 0.001 TRP C 302 HIS 0.007 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 8512) covalent geometry : angle 0.61885 (11685) SS BOND : bond 0.00616 ( 4) SS BOND : angle 3.06831 ( 8) hydrogen bonds : bond 0.03121 ( 703) hydrogen bonds : angle 3.28738 ( 2091) link_ALPHA1-4 : bond 0.00663 ( 1) link_ALPHA1-4 : angle 2.80234 ( 3) link_ALPHA1-6 : bond 0.01638 ( 2) link_ALPHA1-6 : angle 2.40958 ( 6) link_BETA1-3 : bond 0.00963 ( 2) link_BETA1-3 : angle 1.57155 ( 6) link_BETA1-4 : bond 0.00525 ( 1) link_BETA1-4 : angle 4.76772 ( 3) link_NAG-ASN : bond 0.00426 ( 5) link_NAG-ASN : angle 3.47623 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 234 TYR cc_start: 0.7759 (m-80) cc_final: 0.7179 (m-80) REVERT: F 258 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7638 (p0) REVERT: C 235 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8394 (mp) REVERT: C 245 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6296 (mtp) REVERT: C 578 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8417 (m-10) REVERT: C 587 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8133 (tm-30) outliers start: 30 outliers final: 21 residues processed: 143 average time/residue: 0.0640 time to fit residues: 13.2955 Evaluate side-chains 147 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 150 TYR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 539 CYS Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 705 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 41 optimal weight: 30.0000 chunk 125 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 70 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.272759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.245708 restraints weight = 9553.345| |-----------------------------------------------------------------------------| r_work (start): 0.4699 rms_B_bonded: 1.54 r_work: 0.4219 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8527 Z= 0.143 Angle : 0.573 9.286 11726 Z= 0.279 Chirality : 0.041 0.312 1448 Planarity : 0.004 0.047 1568 Dihedral : 9.235 120.789 1615 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.20 % Rotamer: Outliers : 6.16 % Allowed : 26.11 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.24), residues: 1317 helix: 2.44 (0.17), residues: 936 sheet: -1.78 (0.56), residues: 81 loop : -1.39 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 275 TYR 0.014 0.001 TYR F 120 PHE 0.016 0.001 PHE C 706 TRP 0.007 0.001 TRP C 302 HIS 0.004 0.001 HIS C 674 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8512) covalent geometry : angle 0.54673 (11685) SS BOND : bond 0.00369 ( 4) SS BOND : angle 3.10887 ( 8) hydrogen bonds : bond 0.02720 ( 703) hydrogen bonds : angle 3.03910 ( 2091) link_ALPHA1-4 : bond 0.00508 ( 1) link_ALPHA1-4 : angle 3.17361 ( 3) link_ALPHA1-6 : bond 0.01764 ( 2) link_ALPHA1-6 : angle 2.80385 ( 6) link_BETA1-3 : bond 0.00843 ( 2) link_BETA1-3 : angle 1.55802 ( 6) link_BETA1-4 : bond 0.00790 ( 1) link_BETA1-4 : angle 4.12706 ( 3) link_NAG-ASN : bond 0.00434 ( 5) link_NAG-ASN : angle 2.98852 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 234 TYR cc_start: 0.7761 (m-80) cc_final: 0.7091 (m-80) REVERT: F 258 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7652 (p0) REVERT: C 235 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8389 (mp) REVERT: C 587 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8104 (tm-30) outliers start: 29 outliers final: 21 residues processed: 142 average time/residue: 0.0582 time to fit residues: 12.0511 Evaluate side-chains 152 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 150 TYR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 539 CYS Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 705 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 50.0000 chunk 65 optimal weight: 8.9990 chunk 25 optimal weight: 80.0000 chunk 89 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 7 optimal weight: 40.0000 chunk 91 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.271892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.245696 restraints weight = 9429.598| |-----------------------------------------------------------------------------| r_work (start): 0.4698 rms_B_bonded: 1.47 r_work: 0.4198 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8527 Z= 0.163 Angle : 0.593 9.328 11726 Z= 0.289 Chirality : 0.042 0.312 1448 Planarity : 0.004 0.046 1568 Dihedral : 9.035 121.513 1615 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.10 % Allowed : 27.60 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.24), residues: 1317 helix: 2.52 (0.17), residues: 936 sheet: -1.87 (0.55), residues: 82 loop : -1.30 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 116 TYR 0.016 0.001 TYR C 571 PHE 0.027 0.001 PHE C 706 TRP 0.014 0.002 TRP F 121 HIS 0.004 0.001 HIS C 674 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8512) covalent geometry : angle 0.56687 (11685) SS BOND : bond 0.00421 ( 4) SS BOND : angle 2.91329 ( 8) hydrogen bonds : bond 0.02766 ( 703) hydrogen bonds : angle 3.03541 ( 2091) link_ALPHA1-4 : bond 0.00419 ( 1) link_ALPHA1-4 : angle 3.13822 ( 3) link_ALPHA1-6 : bond 0.01579 ( 2) link_ALPHA1-6 : angle 2.57691 ( 6) link_BETA1-3 : bond 0.00931 ( 2) link_BETA1-3 : angle 1.56765 ( 6) link_BETA1-4 : bond 0.00697 ( 1) link_BETA1-4 : angle 4.05570 ( 3) link_NAG-ASN : bond 0.00415 ( 5) link_NAG-ASN : angle 3.34483 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 116 ARG cc_start: 0.7577 (tpt90) cc_final: 0.7312 (tpt170) REVERT: F 234 TYR cc_start: 0.7658 (m-80) cc_final: 0.6887 (m-80) REVERT: F 258 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7655 (p0) REVERT: C 235 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8452 (mp) REVERT: C 587 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8099 (tm-30) outliers start: 24 outliers final: 21 residues processed: 145 average time/residue: 0.0644 time to fit residues: 13.3590 Evaluate side-chains 148 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 539 CYS Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 705 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 40.0000 chunk 98 optimal weight: 30.0000 chunk 112 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 0 optimal weight: 60.0000 chunk 86 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.269983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.247653 restraints weight = 9439.084| |-----------------------------------------------------------------------------| r_work (start): 0.4716 rms_B_bonded: 1.22 r_work: 0.4270 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 8527 Z= 0.252 Angle : 0.643 9.367 11726 Z= 0.319 Chirality : 0.044 0.326 1448 Planarity : 0.004 0.052 1568 Dihedral : 9.178 121.565 1615 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 6.79 % Allowed : 26.54 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.24), residues: 1317 helix: 2.32 (0.17), residues: 934 sheet: -2.02 (0.53), residues: 82 loop : -1.31 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 132 TYR 0.024 0.002 TYR C 571 PHE 0.017 0.002 PHE C 706 TRP 0.019 0.002 TRP F 121 HIS 0.006 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 8512) covalent geometry : angle 0.62073 (11685) SS BOND : bond 0.00348 ( 4) SS BOND : angle 3.38752 ( 8) hydrogen bonds : bond 0.03135 ( 703) hydrogen bonds : angle 3.28149 ( 2091) link_ALPHA1-4 : bond 0.00325 ( 1) link_ALPHA1-4 : angle 2.95398 ( 3) link_ALPHA1-6 : bond 0.01803 ( 2) link_ALPHA1-6 : angle 2.42660 ( 6) link_BETA1-3 : bond 0.00924 ( 2) link_BETA1-3 : angle 1.61363 ( 6) link_BETA1-4 : bond 0.00682 ( 1) link_BETA1-4 : angle 3.84918 ( 3) link_NAG-ASN : bond 0.00409 ( 5) link_NAG-ASN : angle 3.00352 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 234 TYR cc_start: 0.8171 (m-80) cc_final: 0.7295 (m-80) REVERT: F 258 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7728 (p0) REVERT: C 235 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8600 (mp) REVERT: C 245 MET cc_start: 0.6843 (mtp) cc_final: 0.6573 (mtp) REVERT: C 578 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.8583 (m-10) REVERT: C 587 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: C 675 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7735 (pt0) outliers start: 32 outliers final: 22 residues processed: 150 average time/residue: 0.0591 time to fit residues: 13.1602 Evaluate side-chains 150 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 150 TYR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 705 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 123 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 22 optimal weight: 50.0000 chunk 82 optimal weight: 0.8980 chunk 75 optimal weight: 0.0470 chunk 95 optimal weight: 8.9990 chunk 39 optimal weight: 40.0000 chunk 23 optimal weight: 0.0870 chunk 87 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 30.0000 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.274449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.249065 restraints weight = 9380.738| |-----------------------------------------------------------------------------| r_work (start): 0.4736 rms_B_bonded: 1.43 r_work: 0.4269 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8527 Z= 0.114 Angle : 0.555 9.418 11726 Z= 0.274 Chirality : 0.040 0.347 1448 Planarity : 0.004 0.046 1568 Dihedral : 8.813 122.170 1615 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.67 % Allowed : 28.24 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.24), residues: 1317 helix: 2.63 (0.17), residues: 939 sheet: -1.97 (0.55), residues: 82 loop : -1.29 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 116 TYR 0.017 0.001 TYR F 120 PHE 0.026 0.001 PHE C 706 TRP 0.010 0.002 TRP F 121 HIS 0.003 0.001 HIS C 674 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8512) covalent geometry : angle 0.53317 (11685) SS BOND : bond 0.00603 ( 4) SS BOND : angle 2.43771 ( 8) hydrogen bonds : bond 0.02596 ( 703) hydrogen bonds : angle 2.91567 ( 2091) link_ALPHA1-4 : bond 0.00394 ( 1) link_ALPHA1-4 : angle 3.38132 ( 3) link_ALPHA1-6 : bond 0.01433 ( 2) link_ALPHA1-6 : angle 2.48605 ( 6) link_BETA1-3 : bond 0.00809 ( 2) link_BETA1-3 : angle 1.64819 ( 6) link_BETA1-4 : bond 0.00719 ( 1) link_BETA1-4 : angle 3.70122 ( 3) link_NAG-ASN : bond 0.00434 ( 5) link_NAG-ASN : angle 2.78572 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: F 234 TYR cc_start: 0.7490 (m-80) cc_final: 0.6896 (m-80) REVERT: F 258 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7565 (p0) REVERT: C 223 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7730 (mm-30) REVERT: C 587 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: C 675 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7520 (pt0) outliers start: 22 outliers final: 15 residues processed: 145 average time/residue: 0.0619 time to fit residues: 13.0515 Evaluate side-chains 144 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 539 CYS Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain C residue 705 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 52 optimal weight: 0.6980 chunk 1 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 50.0000 chunk 29 optimal weight: 0.5980 chunk 67 optimal weight: 0.0170 chunk 51 optimal weight: 50.0000 chunk 84 optimal weight: 0.8980 chunk 12 optimal weight: 30.0000 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.274333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.246804 restraints weight = 9400.025| |-----------------------------------------------------------------------------| r_work (start): 0.4714 rms_B_bonded: 1.57 r_work: 0.4205 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8527 Z= 0.125 Angle : 0.549 9.342 11726 Z= 0.271 Chirality : 0.041 0.345 1448 Planarity : 0.004 0.045 1568 Dihedral : 8.552 122.551 1615 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.03 % Allowed : 28.24 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.24), residues: 1317 helix: 2.74 (0.17), residues: 940 sheet: -1.96 (0.54), residues: 82 loop : -1.32 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 600 TYR 0.018 0.001 TYR C 234 PHE 0.024 0.001 PHE C 706 TRP 0.016 0.002 TRP F 121 HIS 0.004 0.001 HIS C 674 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8512) covalent geometry : angle 0.53082 (11685) SS BOND : bond 0.00438 ( 4) SS BOND : angle 2.12915 ( 8) hydrogen bonds : bond 0.02552 ( 703) hydrogen bonds : angle 2.85692 ( 2091) link_ALPHA1-4 : bond 0.00286 ( 1) link_ALPHA1-4 : angle 3.19334 ( 3) link_ALPHA1-6 : bond 0.01387 ( 2) link_ALPHA1-6 : angle 1.90340 ( 6) link_BETA1-3 : bond 0.00786 ( 2) link_BETA1-3 : angle 1.67126 ( 6) link_BETA1-4 : bond 0.00564 ( 1) link_BETA1-4 : angle 3.44395 ( 3) link_NAG-ASN : bond 0.00427 ( 5) link_NAG-ASN : angle 2.61895 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1587.19 seconds wall clock time: 27 minutes 45.61 seconds (1665.61 seconds total)